Starting phenix.real_space_refine on Thu Jul 24 14:07:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmu_34154/07_2025/8gmu_34154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmu_34154/07_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_34154/07_2025/8gmu_34154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmu_34154/07_2025/8gmu_34154.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmu_34154/07_2025/8gmu_34154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmu_34154/07_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-5711/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: 4.41, per 1000 atoms: 0.71 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: 1.77 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: 0.91 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: 2.24 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.670 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:113.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.670 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15847 ( 308) hydrogen bonds : angle 5.85839 ( 846) covalent geometry : bond 0.00302 ( 6315) covalent geometry : angle 0.54572 ( 8551) *********************** 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 : 1.617 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: 1.7850 time to fit residues: 176.6063 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 : 0.644 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.160447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119549 restraints weight = 6290.560| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.33 r_work: 0.3080 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0657 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= 0.142 Angle : 0.522 5.620 8551 Z= 0.282 Chirality : 0.043 0.149 971 Planarity : 0.004 0.052 1083 Dihedral : 13.898 167.693 954 Min Nonbonded Distance : 1.969 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 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 308) hydrogen bonds : angle 4.45586 ( 846) covalent geometry : bond 0.00321 ( 6315) covalent geometry : angle 0.52173 ( 8551) *********************** 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 : 0.796 Fit side-chains REVERT: A 101 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: A 113 MET cc_start: 0.6338 (ttp) cc_final: 0.6085 (ttt) REVERT: A 149 SER cc_start: 0.8024 (p) cc_final: 0.7792 (t) REVERT: A 200 GLN cc_start: 0.6043 (OUTLIER) cc_final: 0.5835 (mt0) REVERT: F 184 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7400 (tm-30) REVERT: F 271 TYR cc_start: 0.7921 (m-10) cc_final: 0.7518 (m-80) REVERT: G 31 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6990 (pm20) outliers start: 21 outliers final: 10 residues processed: 101 average time/residue: 2.3403 time to fit residues: 245.7478 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 : 0.716 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.161643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.120804 restraints weight = 6407.491| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.93 r_work: 0.2986 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0907 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= 0.115 Angle : 0.474 4.826 8551 Z= 0.255 Chirality : 0.042 0.148 971 Planarity : 0.003 0.044 1083 Dihedral : 13.397 169.074 950 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 3.14 % Allowed : 21.86 % Favored : 75.00 % 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: 2.08 (0.29), residues: 292 sheet: 1.25 (0.42), residues: 143 loop : -0.38 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 G 85 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 308) hydrogen bonds : angle 4.18235 ( 846) covalent geometry : bond 0.00261 ( 6315) covalent geometry : angle 0.47378 ( 8551) *********************** 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 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 2.204 Fit side-chains REVERT: A 101 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: A 102 GLU cc_start: 0.7651 (pt0) cc_final: 0.7255 (pt0) REVERT: A 103 TYR cc_start: 0.8586 (m-80) cc_final: 0.8374 (m-80) REVERT: A 113 MET cc_start: 0.6214 (ttp) cc_final: 0.5953 (ttt) REVERT: A 131 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7322 (m) REVERT: A 149 SER cc_start: 0.8050 (p) cc_final: 0.7797 (t) REVERT: A 200 GLN cc_start: 0.6077 (OUTLIER) cc_final: 0.5875 (mt0) REVERT: A 217 GLU cc_start: 0.8114 (mp0) cc_final: 0.7886 (mt-10) REVERT: F 184 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7389 (tm-30) REVERT: F 197 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7991 (ppp) REVERT: F 271 TYR cc_start: 0.8042 (m-10) cc_final: 0.7620 (m-80) outliers start: 20 outliers final: 10 residues processed: 96 average time/residue: 1.6710 time to fit residues: 170.0383 Evaluate side-chains 97 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.160092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.119041 restraints weight = 6453.913| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.93 r_work: 0.2966 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1059 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= 0.143 Angle : 0.498 4.991 8551 Z= 0.266 Chirality : 0.043 0.166 971 Planarity : 0.004 0.040 1083 Dihedral : 13.365 170.974 946 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % Rotamer: Outliers : 3.77 % Allowed : 21.86 % 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: 1.15 (0.30), residues: 791 helix: 2.01 (0.29), residues: 292 sheet: 0.83 (0.41), residues: 155 loop : -0.33 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 308 HIS 0.002 0.001 HIS F 163 PHE 0.011 0.001 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.002 0.000 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 308) hydrogen bonds : angle 4.13699 ( 846) covalent geometry : bond 0.00331 ( 6315) covalent geometry : angle 0.49785 ( 8551) *********************** 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 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.743 Fit side-chains REVERT: A 101 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: A 102 GLU cc_start: 0.7689 (pt0) cc_final: 0.7349 (pt0) REVERT: A 113 MET cc_start: 0.6248 (ttp) cc_final: 0.5996 (ttt) REVERT: A 131 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7369 (m) REVERT: A 212 MET cc_start: 0.7882 (mtm) cc_final: 0.7378 (mmm) REVERT: A 217 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: F 27 MET cc_start: 0.7912 (ptm) cc_final: 0.7696 (ptm) REVERT: F 184 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7414 (tm-30) REVERT: F 197 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7987 (ppp) REVERT: F 271 TYR cc_start: 0.7973 (m-10) cc_final: 0.7637 (m-80) outliers start: 24 outliers final: 10 residues processed: 97 average time/residue: 2.2056 time to fit residues: 223.6186 Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 48 optimal weight: 0.0570 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 0.0470 chunk 4 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.163031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.121631 restraints weight = 6376.347| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.40 r_work: 0.3113 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1258 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= 0.092 Angle : 0.439 4.557 8551 Z= 0.238 Chirality : 0.041 0.138 971 Planarity : 0.003 0.036 1083 Dihedral : 13.038 170.956 946 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.01 % Favored : 98.86 % Rotamer: Outliers : 2.52 % Allowed : 23.43 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.30), residues: 791 helix: 2.40 (0.30), residues: 280 sheet: 0.87 (0.41), residues: 158 loop : -0.25 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 129 HIS 0.002 0.001 HIS F 163 PHE 0.007 0.001 PHE G 260 TYR 0.005 0.001 TYR F 65 ARG 0.001 0.000 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.02789 ( 308) hydrogen bonds : angle 4.02070 ( 846) covalent geometry : bond 0.00207 ( 6315) covalent geometry : angle 0.43876 ( 8551) *********************** 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 98 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.878 Fit side-chains REVERT: A 101 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7088 (m-80) REVERT: A 102 GLU cc_start: 0.7558 (pt0) cc_final: 0.7333 (pt0) REVERT: A 113 MET cc_start: 0.5813 (ttp) cc_final: 0.5609 (ttt) REVERT: A 117 GLU cc_start: 0.7146 (tp30) cc_final: 0.6864 (tm-30) REVERT: A 212 MET cc_start: 0.7900 (mtm) cc_final: 0.7376 (mmm) REVERT: A 217 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: A 229 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7083 (mt0) REVERT: F 27 MET cc_start: 0.7895 (ptm) cc_final: 0.7632 (ptm) REVERT: F 184 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7371 (tm-30) REVERT: F 197 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7972 (ppp) REVERT: F 271 TYR cc_start: 0.7888 (m-10) cc_final: 0.7585 (m-80) REVERT: G 183 LYS cc_start: 0.8346 (tppp) cc_final: 0.7595 (tptp) outliers start: 16 outliers final: 9 residues processed: 90 average time/residue: 1.4077 time to fit residues: 133.7686 Evaluate side-chains 91 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 A residue 229 GLN 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 283 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 10 optimal weight: 0.0370 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.0060 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.162071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.120653 restraints weight = 6298.082| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.97 r_work: 0.2990 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1301 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= 0.113 Angle : 0.456 5.893 8551 Z= 0.245 Chirality : 0.042 0.149 971 Planarity : 0.003 0.036 1083 Dihedral : 12.967 173.944 943 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 3.14 % Allowed : 23.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.30), residues: 791 helix: 2.23 (0.29), residues: 292 sheet: 1.00 (0.42), residues: 155 loop : -0.26 (0.34), residues: 344 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 0.009 0.001 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.001 0.000 ARG F 243 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 308) hydrogen bonds : angle 3.99374 ( 846) covalent geometry : bond 0.00259 ( 6315) covalent geometry : angle 0.45611 ( 8551) *********************** 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 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.644 Fit side-chains REVERT: A 101 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: A 102 GLU cc_start: 0.7649 (pt0) cc_final: 0.7407 (pt0) REVERT: A 113 MET cc_start: 0.5937 (ttp) cc_final: 0.5694 (ttt) REVERT: A 117 GLU cc_start: 0.7187 (tp30) cc_final: 0.6944 (tm-30) REVERT: A 131 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7544 (m) REVERT: A 212 MET cc_start: 0.7884 (mtm) cc_final: 0.7309 (mmm) REVERT: A 217 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7871 (mt-10) REVERT: A 229 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7125 (mt0) REVERT: F 27 MET cc_start: 0.7908 (ptm) cc_final: 0.7621 (ptm) REVERT: F 184 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7447 (tm-30) REVERT: F 197 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7978 (ppp) REVERT: F 226 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8253 (mtt-85) REVERT: F 271 TYR cc_start: 0.7940 (m-10) cc_final: 0.7619 (m-80) REVERT: G 183 LYS cc_start: 0.8399 (tppp) cc_final: 0.7703 (tptp) outliers start: 20 outliers final: 7 residues processed: 92 average time/residue: 1.3897 time to fit residues: 133.4206 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 : 0.734 ------------------------------------------------------------------------------- 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 217 GLU Chi-restraints excluded: chain A residue 229 GLN 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 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 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: 6.9990 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.158666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.112450 restraints weight = 6331.012| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.36 r_work: 0.3010 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.006 0.039 6315 Z= 0.233 Angle : 0.593 5.636 8551 Z= 0.309 Chirality : 0.047 0.249 971 Planarity : 0.005 0.043 1083 Dihedral : 13.539 173.848 942 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.60 % 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: 0.94 (0.29), residues: 791 helix: 1.91 (0.30), residues: 280 sheet: 0.67 (0.41), residues: 155 loop : -0.41 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.003 0.001 HIS F 163 PHE 0.014 0.002 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.007 0.001 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 308) hydrogen bonds : angle 4.19382 ( 846) covalent geometry : bond 0.00554 ( 6315) covalent geometry : angle 0.59347 ( 8551) *********************** 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 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.806 Fit side-chains REVERT: A 101 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: A 113 MET cc_start: 0.6170 (ttp) cc_final: 0.5923 (ttt) REVERT: A 131 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7513 (m) REVERT: A 212 MET cc_start: 0.7846 (mtm) cc_final: 0.7355 (mmm) REVERT: A 217 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: A 229 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: F 27 MET cc_start: 0.7946 (ptm) cc_final: 0.7690 (ptm) REVERT: F 226 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8446 (mtt-85) REVERT: F 271 TYR cc_start: 0.7890 (m-10) cc_final: 0.7570 (m-80) REVERT: G 120 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: G 332 ASN cc_start: 0.0120 (OUTLIER) cc_final: -0.0802 (p0) outliers start: 25 outliers final: 13 residues processed: 94 average time/residue: 1.4313 time to fit residues: 140.4088 Evaluate side-chains 102 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 229 GLN 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 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.161879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.120810 restraints weight = 6301.426| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.98 r_work: 0.2986 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6315 Z= 0.108 Angle : 0.465 6.826 8551 Z= 0.251 Chirality : 0.042 0.173 971 Planarity : 0.003 0.036 1083 Dihedral : 13.211 172.996 942 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.74 % Rotamer: Outliers : 3.14 % Allowed : 23.90 % 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 (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: 2.13 (0.30), residues: 280 sheet: 0.71 (0.41), residues: 157 loop : -0.32 (0.33), residues: 354 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 0.009 0.001 PHE G 260 TYR 0.007 0.001 TYR F 103 ARG 0.002 0.000 ARG G 169 Details of bonding type rmsd hydrogen bonds : bond 0.02967 ( 308) hydrogen bonds : angle 4.05985 ( 846) covalent geometry : bond 0.00246 ( 6315) covalent geometry : angle 0.46513 ( 8551) *********************** 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 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.812 Fit side-chains REVERT: A 101 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: A 102 GLU cc_start: 0.7670 (pt0) cc_final: 0.7444 (pt0) REVERT: A 103 TYR cc_start: 0.8564 (m-80) cc_final: 0.8329 (m-80) REVERT: A 113 MET cc_start: 0.6006 (ttp) cc_final: 0.5792 (ttt) REVERT: A 131 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7536 (m) REVERT: A 217 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: A 229 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: F 27 MET cc_start: 0.7882 (ptm) cc_final: 0.7593 (ptm) REVERT: F 28 ARG cc_start: 0.7987 (mpt180) cc_final: 0.7757 (mpt180) REVERT: F 96 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6275 (mm-30) REVERT: F 226 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8231 (mtt-85) REVERT: F 271 TYR cc_start: 0.7939 (m-10) cc_final: 0.7642 (m-80) outliers start: 20 outliers final: 9 residues processed: 94 average time/residue: 1.7049 time to fit residues: 166.6474 Evaluate side-chains 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 76 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.159149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.115539 restraints weight = 6396.794| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.37 r_work: 0.3034 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1435 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= 0.188 Angle : 0.546 6.259 8551 Z= 0.287 Chirality : 0.045 0.236 971 Planarity : 0.004 0.038 1083 Dihedral : 13.402 174.363 942 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.15 % Favored : 97.72 % Rotamer: Outliers : 3.30 % Allowed : 23.43 % 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: 0.95 (0.30), residues: 791 helix: 1.96 (0.30), residues: 280 sheet: 0.70 (0.41), residues: 155 loop : -0.46 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 129 HIS 0.004 0.001 HIS F 163 PHE 0.012 0.002 PHE G 203 TYR 0.007 0.001 TYR F 103 ARG 0.005 0.001 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 308) hydrogen bonds : angle 4.14873 ( 846) covalent geometry : bond 0.00443 ( 6315) covalent geometry : angle 0.54586 ( 8551) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.967 Fit side-chains REVERT: A 101 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: A 113 MET cc_start: 0.6190 (ttp) cc_final: 0.5959 (ttt) REVERT: A 131 SER cc_start: 0.7808 (OUTLIER) cc_final: 0.7456 (m) REVERT: A 217 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: F 27 MET cc_start: 0.7952 (ptm) cc_final: 0.7669 (ptm) REVERT: F 96 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6322 (mm-30) REVERT: F 111 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7915 (pt) REVERT: F 226 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8294 (mtt-85) REVERT: F 271 TYR cc_start: 0.7892 (m-10) cc_final: 0.7655 (m-80) outliers start: 21 outliers final: 13 residues processed: 92 average time/residue: 1.5152 time to fit residues: 145.3370 Evaluate side-chains 101 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 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 197 MET Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 226 ARG Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 31 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 0.0270 chunk 44 optimal weight: 2.9990 overall best weight: 2.1444 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.159416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117676 restraints weight = 6400.724| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.95 r_work: 0.2924 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6315 Z= 0.178 Angle : 0.534 7.071 8551 Z= 0.283 Chirality : 0.045 0.235 971 Planarity : 0.004 0.038 1083 Dihedral : 13.504 174.493 942 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.90 % Favored : 97.98 % Rotamer: Outliers : 3.62 % Allowed : 22.96 % 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: 0.88 (0.29), residues: 791 helix: 1.90 (0.30), residues: 280 sheet: 0.93 (0.42), residues: 144 loop : -0.59 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 129 HIS 0.004 0.001 HIS F 163 PHE 0.013 0.002 PHE G 203 TYR 0.008 0.001 TYR F 103 ARG 0.004 0.001 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 308) hydrogen bonds : angle 4.15165 ( 846) covalent geometry : bond 0.00417 ( 6315) covalent geometry : angle 0.53442 ( 8551) ********************** 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 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.690 Fit side-chains REVERT: A 101 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: A 113 MET cc_start: 0.6192 (ttp) cc_final: 0.5990 (ttt) REVERT: A 131 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7557 (m) REVERT: A 217 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: A 229 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7521 (mt0) REVERT: F 27 MET cc_start: 0.7959 (ptm) cc_final: 0.7689 (ptm) REVERT: F 111 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7945 (pt) REVERT: F 226 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8412 (mtt-85) REVERT: F 271 TYR cc_start: 0.7925 (m-10) cc_final: 0.7695 (m-80) outliers start: 23 outliers final: 13 residues processed: 92 average time/residue: 1.3761 time to fit residues: 132.2443 Evaluate side-chains 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 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 149 SER Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 229 GLN 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 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 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.158842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.118847 restraints weight = 6459.462| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.82 r_work: 0.2878 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6315 Z= 0.192 Angle : 0.555 6.831 8551 Z= 0.292 Chirality : 0.045 0.249 971 Planarity : 0.004 0.038 1083 Dihedral : 13.639 174.244 942 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.60 % 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 (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: 0.79 (0.29), residues: 791 helix: 1.83 (0.30), residues: 280 sheet: 0.87 (0.42), residues: 144 loop : -0.64 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 129 HIS 0.004 0.001 HIS F 163 PHE 0.014 0.002 PHE G 203 TYR 0.007 0.001 TYR F 103 ARG 0.005 0.001 ARG F 226 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 308) hydrogen bonds : angle 4.18990 ( 846) covalent geometry : bond 0.00452 ( 6315) covalent geometry : angle 0.55540 ( 8551) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6107.46 seconds wall clock time: 111 minutes 7.91 seconds (6667.91 seconds total)