Starting phenix.real_space_refine on Tue Feb 11 16:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmu_34154/02_2025/8gmu_34154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmu_34154/02_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_34154/02_2025/8gmu_34154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmu_34154/02_2025/8gmu_34154.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmu_34154/02_2025/8gmu_34154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmu_34154/02_2025/8gmu_34154.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.00, per 1000 atoms: 0.80 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: 1.42 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.77 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: 2.18 Time building geometry restraints manager: 1.67 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: 1.360 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: 0.490 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.950 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- 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= 0.197 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (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 TRP 0.017 0.002 TRP F 308 HIS 0.003 0.001 HIS F 163 PHE 0.008 0.001 PHE A 114 TYR 0.005 0.001 TYR F 271 ARG 0.003 0.000 ARG G 85 *********************** 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 : 0.796 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: 1.5011 time to fit residues: 148.8984 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 : 0.919 ------------------------------------------------------------------------------- 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 66 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.0270 chunk 71 optimal weight: 2.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- 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 = 0.3708 r_free = 0.3708 target = 0.160609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119729 restraints weight = 6287.895| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.33 r_work: 0.3076 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6315 Z= 0.211 Angle : 0.522 5.619 8551 Z= 0.282 Chirality : 0.043 0.149 971 Planarity : 0.004 0.052 1083 Dihedral : 13.902 167.690 954 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.64 % Favored : 98.23 % Rotamer: Outliers : 3.30 % Allowed : 21.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.30), residues: 791 helix: 1.89 (0.29), residues: 292 sheet: 1.48 (0.43), residues: 132 loop : -0.46 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 308 HIS 0.002 0.001 HIS F 163 PHE 0.008 0.001 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.002 0.000 ARG A 196 *********************** 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 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.655 Fit side-chains REVERT: A 101 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: A 113 MET cc_start: 0.6343 (ttp) cc_final: 0.6093 (ttt) REVERT: A 149 SER cc_start: 0.8032 (p) cc_final: 0.7807 (t) REVERT: A 200 GLN cc_start: 0.6082 (OUTLIER) cc_final: 0.5877 (mt0) REVERT: F 184 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7404 (tm-30) REVERT: F 271 TYR cc_start: 0.7937 (m-10) cc_final: 0.7537 (m-80) REVERT: G 31 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6995 (pm20) outliers start: 21 outliers final: 10 residues processed: 101 average time/residue: 1.4148 time to fit residues: 149.0805 Evaluate side-chains 96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 200 GLN 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 196 ARG Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain G residue 31 GLU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN F 213 ASN G 118 GLN G 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.160256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.119999 restraints weight = 6407.417| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.92 r_work: 0.2968 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0929 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= 0.213 Angle : 0.503 5.163 8551 Z= 0.268 Chirality : 0.043 0.165 971 Planarity : 0.004 0.044 1083 Dihedral : 13.623 169.884 950 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 3.46 % Allowed : 21.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 791 helix: 1.95 (0.29), residues: 292 sheet: 1.14 (0.42), residues: 143 loop : -0.42 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 308 HIS 0.003 0.001 HIS F 163 PHE 0.010 0.001 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.002 0.000 ARG F 227 *********************** 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 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.728 Fit side-chains REVERT: A 101 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: A 102 GLU cc_start: 0.7666 (pt0) cc_final: 0.7243 (pt0) REVERT: A 113 MET cc_start: 0.6380 (ttp) cc_final: 0.6128 (ttt) REVERT: A 131 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7378 (m) REVERT: A 149 SER cc_start: 0.8145 (p) cc_final: 0.7896 (t) REVERT: A 200 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5982 (mt0) REVERT: F 184 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7416 (tm-30) REVERT: F 197 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8066 (ppp) REVERT: F 271 TYR cc_start: 0.8019 (m-10) cc_final: 0.7595 (m-80) outliers start: 22 outliers final: 12 residues processed: 97 average time/residue: 1.4008 time to fit residues: 142.2866 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 : 0.720 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 200 GLN 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 197 MET Chi-restraints excluded: chain F residue 199 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.0170 chunk 23 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 = 0.161869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.120939 restraints weight = 6444.227| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.94 r_work: 0.3002 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6315 Z= 0.146 Angle : 0.455 4.653 8551 Z= 0.247 Chirality : 0.042 0.142 971 Planarity : 0.003 0.039 1083 Dihedral : 13.229 169.769 946 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.74 % Rotamer: Outliers : 3.30 % Allowed : 22.33 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.30), residues: 791 helix: 2.16 (0.30), residues: 292 sheet: 0.82 (0.41), residues: 157 loop : -0.28 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.002 0.001 HIS F 97 PHE 0.008 0.001 PHE G 260 TYR 0.005 0.001 TYR F 103 ARG 0.001 0.000 ARG G 243 *********************** 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: 21 poor density : 84 time to evaluate : 0.721 Fit side-chains REVERT: A 101 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: A 102 GLU cc_start: 0.7571 (pt0) cc_final: 0.7191 (pt0) REVERT: A 113 MET cc_start: 0.6159 (ttp) cc_final: 0.5921 (ttt) REVERT: A 131 SER cc_start: 0.7828 (OUTLIER) cc_final: 0.7427 (m) REVERT: A 217 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: F 184 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7444 (tm-30) REVERT: F 197 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8051 (ppp) REVERT: F 271 TYR cc_start: 0.7977 (m-10) cc_final: 0.7640 (m-80) outliers start: 21 outliers final: 8 residues processed: 95 average time/residue: 1.3469 time to fit residues: 133.9434 Evaluate side-chains 92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 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 197 MET Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3717 r_free = 0.3717 target = 0.161603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120673 restraints weight = 6371.579| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.51 r_work: 0.3083 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6315 Z= 0.174 Angle : 0.461 5.308 8551 Z= 0.248 Chirality : 0.042 0.148 971 Planarity : 0.003 0.037 1083 Dihedral : 13.052 172.548 943 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 3.14 % Allowed : 23.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.30), residues: 791 helix: 2.17 (0.29), residues: 292 sheet: 0.89 (0.41), residues: 155 loop : -0.30 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.003 0.001 HIS F 97 PHE 0.008 0.001 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.001 0.000 ARG A 183 *********************** 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 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.763 Fit side-chains REVERT: A 101 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7072 (m-80) REVERT: A 102 GLU cc_start: 0.7617 (pt0) cc_final: 0.7320 (pt0) REVERT: A 113 MET cc_start: 0.5902 (ttp) cc_final: 0.5652 (ttt) REVERT: A 131 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7423 (m) REVERT: A 134 LYS cc_start: 0.7852 (tptm) cc_final: 0.7557 (tptt) REVERT: A 212 MET cc_start: 0.7896 (mtm) cc_final: 0.7339 (mmm) REVERT: A 217 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: F 102 ILE cc_start: 0.8498 (mm) cc_final: 0.8274 (mp) REVERT: F 184 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7395 (tm-30) REVERT: F 197 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7981 (ppp) REVERT: F 226 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8305 (mtt-85) REVERT: F 271 TYR cc_start: 0.7903 (m-10) cc_final: 0.7575 (m-80) REVERT: G 183 LYS cc_start: 0.8401 (tppp) cc_final: 0.7673 (tptp) outliers start: 20 outliers final: 12 residues processed: 97 average time/residue: 1.4437 time to fit residues: 146.2699 Evaluate side-chains 100 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 GLU 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 197 MET Chi-restraints excluded: chain F residue 199 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 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 = 0.3748 r_free = 0.3748 target = 0.163866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.123084 restraints weight = 6345.170| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.99 r_work: 0.3005 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1356 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= 0.145 Angle : 0.441 5.321 8551 Z= 0.239 Chirality : 0.041 0.136 971 Planarity : 0.003 0.035 1083 Dihedral : 12.934 173.544 943 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.74 % Rotamer: Outliers : 2.67 % Allowed : 24.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.30), residues: 791 helix: 2.27 (0.30), residues: 292 sheet: 0.84 (0.41), residues: 159 loop : -0.29 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.002 0.001 HIS F 97 PHE 0.007 0.001 PHE G 260 TYR 0.005 0.001 TYR F 103 ARG 0.001 0.000 ARG G 169 *********************** 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 96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.665 Fit side-chains REVERT: A 101 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: A 102 GLU cc_start: 0.7598 (pt0) cc_final: 0.7323 (pt0) REVERT: A 113 MET cc_start: 0.5841 (ttp) cc_final: 0.5619 (ttt) REVERT: A 114 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.5305 (t80) REVERT: A 134 LYS cc_start: 0.7914 (tptm) cc_final: 0.7687 (tptt) REVERT: A 144 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7019 (pp20) REVERT: A 212 MET cc_start: 0.7885 (mtm) cc_final: 0.7340 (mmm) REVERT: A 217 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: F 184 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7441 (tm-30) REVERT: F 197 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.7997 (ppp) REVERT: F 271 TYR cc_start: 0.7909 (m-10) cc_final: 0.7584 (m-80) outliers start: 17 outliers final: 7 residues processed: 88 average time/residue: 1.3898 time to fit residues: 127.8922 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 : 0.674 ------------------------------------------------------------------------------- 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 217 GLU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 199 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.158106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.116896 restraints weight = 6345.322| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.94 r_work: 0.2917 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6315 Z= 0.405 Angle : 0.613 6.149 8551 Z= 0.318 Chirality : 0.048 0.252 971 Planarity : 0.005 0.047 1083 Dihedral : 13.582 173.682 942 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.40 % Favored : 97.47 % Rotamer: Outliers : 3.46 % Allowed : 22.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 791 helix: 1.85 (0.30), residues: 280 sheet: 0.85 (0.42), residues: 144 loop : -0.49 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 129 HIS 0.003 0.001 HIS F 97 PHE 0.015 0.002 PHE G 203 TYR 0.006 0.002 TYR F 103 ARG 0.007 0.001 ARG F 226 *********************** 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 : 0.702 Fit side-chains REVERT: A 101 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6758 (m-80) REVERT: A 113 MET cc_start: 0.6204 (ttp) cc_final: 0.5952 (ttt) REVERT: A 131 SER cc_start: 0.7903 (OUTLIER) cc_final: 0.7467 (m) REVERT: A 212 MET cc_start: 0.7842 (mtm) cc_final: 0.7373 (mmm) REVERT: A 217 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: F 226 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8432 (mtt-85) REVERT: F 271 TYR cc_start: 0.7941 (m-10) cc_final: 0.7623 (m-80) REVERT: G 120 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: G 332 ASN cc_start: 0.0065 (OUTLIER) cc_final: -0.0883 (p0) outliers start: 22 outliers final: 13 residues processed: 91 average time/residue: 1.4707 time to fit residues: 139.5231 Evaluate side-chains 100 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 144 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 GLU 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 197 MET Chi-restraints excluded: chain F residue 199 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 120 ASP 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 47 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.158895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.117814 restraints weight = 6312.199| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.40 r_work: 0.3048 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1431 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= 0.284 Angle : 0.540 5.428 8551 Z= 0.286 Chirality : 0.045 0.221 971 Planarity : 0.004 0.039 1083 Dihedral : 13.622 173.933 942 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.15 % Favored : 97.72 % Rotamer: Outliers : 3.93 % Allowed : 22.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 791 helix: 1.78 (0.30), residues: 280 sheet: 0.57 (0.40), residues: 155 loop : -0.47 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 129 HIS 0.003 0.001 HIS F 163 PHE 0.012 0.002 PHE G 203 TYR 0.007 0.001 TYR F 103 ARG 0.004 0.001 ARG F 226 *********************** 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: 25 poor density : 82 time to evaluate : 0.684 Fit side-chains REVERT: A 101 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6896 (m-80) REVERT: A 113 MET cc_start: 0.6031 (ttp) cc_final: 0.5818 (ttt) REVERT: A 212 MET cc_start: 0.7828 (mtm) cc_final: 0.7371 (mmm) REVERT: A 217 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: F 111 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7876 (pt) REVERT: F 226 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8395 (mtt-85) REVERT: F 271 TYR cc_start: 0.7800 (m-10) cc_final: 0.7554 (m-80) REVERT: G 332 ASN cc_start: -0.0291 (OUTLIER) cc_final: -0.1004 (t0) outliers start: 25 outliers final: 13 residues processed: 95 average time/residue: 1.4626 time to fit residues: 144.8645 Evaluate side-chains 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR 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 197 MET Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain F residue 283 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.159952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.113794 restraints weight = 6405.081| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.40 r_work: 0.3033 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6315 Z= 0.235 Angle : 0.510 5.355 8551 Z= 0.272 Chirality : 0.044 0.214 971 Planarity : 0.004 0.037 1083 Dihedral : 13.497 174.004 942 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 3.93 % Allowed : 22.48 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.29), residues: 791 helix: 1.93 (0.30), residues: 280 sheet: 0.62 (0.41), residues: 155 loop : -0.45 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 129 HIS 0.003 0.001 HIS F 163 PHE 0.011 0.001 PHE G 203 TYR 0.007 0.001 TYR F 103 ARG 0.003 0.000 ARG F 226 *********************** 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 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.673 Fit side-chains REVERT: A 101 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: A 113 MET cc_start: 0.5998 (ttp) cc_final: 0.5780 (ttt) REVERT: A 131 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7451 (m) REVERT: A 217 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: F 226 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8313 (mtt-85) REVERT: F 271 TYR cc_start: 0.7751 (m-80) cc_final: 0.7515 (m-80) REVERT: G 332 ASN cc_start: -0.0511 (OUTLIER) cc_final: -0.1156 (t0) outliers start: 25 outliers final: 12 residues processed: 95 average time/residue: 1.4567 time to fit residues: 144.1736 Evaluate side-chains 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain F residue 199 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN G 113 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 = 0.3703 r_free = 0.3703 target = 0.160014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.113753 restraints weight = 6423.897| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.42 r_work: 0.3044 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 0.031 6315 Z= 0.220 Angle : 0.501 5.610 8551 Z= 0.268 Chirality : 0.043 0.208 971 Planarity : 0.004 0.037 1083 Dihedral : 13.404 174.427 942 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % Rotamer: Outliers : 2.83 % Allowed : 23.58 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.30), residues: 791 helix: 1.97 (0.30), residues: 280 sheet: 0.68 (0.41), residues: 155 loop : -0.43 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 129 HIS 0.004 0.001 HIS F 163 PHE 0.010 0.001 PHE G 203 TYR 0.008 0.001 TYR F 103 ARG 0.002 0.000 ARG F 226 ********************** 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 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.740 Fit side-chains REVERT: A 101 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: A 113 MET cc_start: 0.5914 (ttp) cc_final: 0.5688 (ttt) REVERT: A 131 SER cc_start: 0.7860 (OUTLIER) cc_final: 0.7430 (m) REVERT: A 193 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8468 (tmmm) REVERT: A 217 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: F 226 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8317 (mtt-85) REVERT: F 271 TYR cc_start: 0.7745 (m-80) cc_final: 0.7511 (m-80) REVERT: G 332 ASN cc_start: -0.0558 (OUTLIER) cc_final: -0.1189 (t0) outliers start: 18 outliers final: 10 residues processed: 90 average time/residue: 1.4595 time to fit residues: 136.8973 Evaluate side-chains 95 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 197 MET Chi-restraints excluded: chain F residue 199 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 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.161628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.120888 restraints weight = 6502.481| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.44 r_work: 0.3087 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: 0.7994 moved from start: 0.1533 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= 0.172 Angle : 0.468 6.147 8551 Z= 0.252 Chirality : 0.042 0.173 971 Planarity : 0.003 0.036 1083 Dihedral : 13.189 174.111 942 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 2.67 % Allowed : 23.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.30), residues: 791 helix: 2.18 (0.30), residues: 280 sheet: 0.77 (0.41), residues: 155 loop : -0.39 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 129 HIS 0.004 0.001 HIS F 163 PHE 0.009 0.001 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.001 0.000 ARG G 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4897.49 seconds wall clock time: 87 minutes 11.72 seconds (5231.72 seconds total)