Starting phenix.real_space_refine on Fri Dec 27 18:03:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmu_34154/12_2024/8gmu_34154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmu_34154/12_2024/8gmu_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_34154/12_2024/8gmu_34154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmu_34154/12_2024/8gmu_34154.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmu_34154/12_2024/8gmu_34154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmu_34154/12_2024/8gmu_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-5532/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: 4.14, per 1000 atoms: 0.67 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: 1.61 Conformation dependent library (CDL) restraints added in 817.5 milliseconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 40.9% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 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: 1.91 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2062 1.36 - 1.51: 1584 1.51 - 1.65: 2614 1.65 - 1.80: 30 1.80 - 1.95: 25 Bond restraints: 6315 Sorted by residual: bond pdb=" CA VAL F 246 " pdb=" CB VAL F 246 " ideal model delta sigma weight residual 1.527 1.538 -0.011 1.31e-02 5.83e+03 7.48e-01 bond pdb=" C GLU A 146 " pdb=" N GLY A 147 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 7.24e-01 bond pdb=" C4' DT S 9 " pdb=" O4' DT S 9 " ideal model delta sigma weight residual 1.450 1.433 0.017 2.00e-02 2.50e+03 7.17e-01 bond pdb=" CB LYS G 198 " pdb=" CG LYS G 198 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.14e-01 bond pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.31e-01 ... (remaining 6310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 8317 1.45 - 2.89: 201 2.89 - 4.34: 26 4.34 - 5.79: 6 5.79 - 7.23: 1 Bond angle restraints: 8551 Sorted by residual: angle pdb=" C LEU A 118 " pdb=" N ARG A 119 " pdb=" CA ARG A 119 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" CA ILE A 195 " pdb=" CB ILE A 195 " pdb=" CG1 ILE A 195 " ideal model delta sigma weight residual 110.40 115.01 -4.61 1.70e+00 3.46e-01 7.37e+00 angle pdb=" CA MET F 197 " pdb=" CB MET F 197 " pdb=" CG MET F 197 " ideal model delta sigma weight residual 114.10 119.36 -5.26 2.00e+00 2.50e-01 6.93e+00 angle pdb=" C4' DT S 9 " pdb=" O4' DT S 9 " pdb=" C1' DT S 9 " ideal model delta sigma weight residual 109.70 106.22 3.48 1.50e+00 4.44e-01 5.38e+00 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 107.76 109.79 -2.03 1.01e+00 9.80e-01 4.05e+00 ... (remaining 8546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 3620 34.21 - 68.43: 202 68.43 - 102.64: 13 102.64 - 136.85: 0 136.85 - 171.07: 2 Dihedral angle restraints: 3837 sinusoidal: 1588 harmonic: 2249 Sorted by residual: dihedral pdb=" O1A AGS G 402 " pdb=" O3A AGS G 402 " pdb=" PA AGS G 402 " pdb=" PB AGS G 402 " ideal model delta sinusoidal sigma weight residual -67.73 103.34 -171.07 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1A AGS F 402 " pdb=" O3A AGS F 402 " pdb=" PA AGS F 402 " pdb=" PB AGS F 402 " ideal model delta sinusoidal sigma weight residual -67.73 80.51 -148.24 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CA VAL A 145 " pdb=" C VAL A 145 " pdb=" N GLU A 146 " pdb=" CA GLU A 146 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 717 0.040 - 0.081: 171 0.081 - 0.121: 75 0.121 - 0.161: 7 0.161 - 0.202: 1 Chirality restraints: 971 Sorted by residual: chirality pdb=" CB THR G 208 " pdb=" CA THR G 208 " pdb=" OG1 THR G 208 " pdb=" CG2 THR G 208 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEU F 309 " pdb=" CB LEU F 309 " pdb=" CD1 LEU F 309 " pdb=" CD2 LEU F 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CG LEU G 309 " pdb=" CB LEU G 309 " pdb=" CD1 LEU G 309 " pdb=" CD2 LEU G 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 968 not shown) Planarity restraints: 1083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 207 " 0.041 5.00e-02 4.00e+02 6.34e-02 6.42e+00 pdb=" N PRO A 208 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 195 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ILE A 195 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE A 195 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 196 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 66 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO F 67 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO F 67 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO F 67 " -0.014 5.00e-02 4.00e+02 ... (remaining 1080 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 39 2.53 - 3.12: 4410 3.12 - 3.72: 9774 3.72 - 4.31: 14137 4.31 - 4.90: 23511 Nonbonded interactions: 51871 Sorted by model distance: nonbonded pdb="MG MG G 401 " pdb=" O2G AGS G 402 " model vdw 1.941 2.170 nonbonded pdb=" OG1 THR G 73 " pdb="MG MG G 401 " model vdw 1.954 2.170 nonbonded pdb="MG MG F 401 " pdb=" O2G AGS F 402 " model vdw 1.957 2.170 nonbonded pdb="MG MG G 401 " pdb=" O1B AGS G 402 " model vdw 1.969 2.170 nonbonded pdb=" OG1 THR F 73 " pdb="MG MG F 401 " model vdw 1.970 2.170 ... (remaining 51866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.960 Find NCS groups from input model: 0.170 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:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- 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 : 0.658 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: 1.4237 time to fit residues: 140.9111 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 : 0.716 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 : 0.698 Fit side-chains REVERT: A 101 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: A 113 MET cc_start: 0.6334 (ttp) cc_final: 0.6103 (ttt) REVERT: F 184 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7325 (tm-30) REVERT: F 271 TYR cc_start: 0.7936 (m-10) cc_final: 0.7525 (m-80) outliers start: 21 outliers final: 10 residues processed: 101 average time/residue: 1.4190 time to fit residues: 149.5636 Evaluate side-chains 93 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR 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 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 39 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0922 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= 0.180 Angle : 0.479 4.909 8551 Z= 0.258 Chirality : 0.042 0.153 971 Planarity : 0.003 0.044 1083 Dihedral : 13.465 169.308 950 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % Rotamer: Outliers : 3.14 % Allowed : 22.01 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.30), residues: 791 helix: 2.05 (0.29), residues: 292 sheet: 1.22 (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 0.009 0.001 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.002 0.000 ARG G 85 *********************** 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 104 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.723 Fit side-chains REVERT: A 101 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: A 102 GLU cc_start: 0.7520 (pt0) cc_final: 0.7182 (pt0) REVERT: A 103 TYR cc_start: 0.8660 (m-80) cc_final: 0.8443 (m-80) REVERT: A 113 MET cc_start: 0.6082 (ttp) cc_final: 0.5848 (ttt) REVERT: A 131 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7405 (m) REVERT: F 184 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7282 (tm-30) REVERT: F 197 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8167 (ppp) REVERT: F 271 TYR cc_start: 0.7935 (m-10) cc_final: 0.7521 (m-80) outliers start: 20 outliers final: 11 residues processed: 95 average time/residue: 1.2467 time to fit residues: 124.3449 Evaluate side-chains 96 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 149 SER Chi-restraints excluded: chain A residue 193 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 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 37 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 76 optimal weight: 0.0770 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1096 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= 0.209 Angle : 0.492 5.001 8551 Z= 0.264 Chirality : 0.043 0.165 971 Planarity : 0.003 0.040 1083 Dihedral : 13.362 170.833 946 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % Rotamer: Outliers : 3.93 % Allowed : 21.86 % Favored : 74.21 % 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: 2.02 (0.29), residues: 292 sheet: 0.82 (0.41), residues: 155 loop : -0.37 (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 97 PHE 0.010 0.001 PHE G 203 TYR 0.006 0.001 TYR F 103 ARG 0.002 0.000 ARG F 226 *********************** 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 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.687 Fit side-chains REVERT: A 101 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: A 113 MET cc_start: 0.6181 (ttp) cc_final: 0.5946 (ttt) REVERT: A 131 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7463 (m) REVERT: A 212 MET cc_start: 0.7643 (mtm) cc_final: 0.7189 (mmm) REVERT: A 217 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: F 27 MET cc_start: 0.7857 (ptm) cc_final: 0.7641 (ptm) REVERT: F 184 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7333 (tm-30) REVERT: F 197 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8085 (ppp) REVERT: F 271 TYR cc_start: 0.7908 (m-10) cc_final: 0.7586 (m-80) outliers start: 25 outliers final: 13 residues processed: 98 average time/residue: 1.4076 time to fit residues: 144.0100 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 : 0.719 ------------------------------------------------------------------------------- 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 144 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.0170 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.1424 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1190 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= 0.182 Angle : 0.471 5.257 8551 Z= 0.252 Chirality : 0.042 0.157 971 Planarity : 0.003 0.037 1083 Dihedral : 13.232 171.865 946 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.39 % Favored : 98.48 % Rotamer: Outliers : 3.46 % Allowed : 22.64 % 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: 1.21 (0.30), residues: 791 helix: 2.09 (0.29), residues: 292 sheet: 0.86 (0.41), residues: 155 loop : -0.34 (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 0.002 0.000 ARG G 169 *********************** 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: 22 poor density : 85 time to evaluate : 0.522 Fit side-chains REVERT: A 101 TYR cc_start: 0.7604 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: A 117 GLU cc_start: 0.7293 (tp30) cc_final: 0.7022 (tm-30) REVERT: A 212 MET cc_start: 0.7854 (mtm) cc_final: 0.7302 (mmm) REVERT: A 217 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: A 229 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7242 (mt0) REVERT: F 27 MET cc_start: 0.7871 (ptm) cc_final: 0.7608 (ptm) REVERT: F 102 ILE cc_start: 0.8654 (mm) cc_final: 0.8429 (mp) REVERT: F 111 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7880 (pt) REVERT: F 184 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7328 (tm-30) REVERT: F 197 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8045 (ppp) REVERT: F 226 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8312 (mtt-85) REVERT: F 271 TYR cc_start: 0.7868 (m-10) cc_final: 0.7565 (m-80) outliers start: 22 outliers final: 13 residues processed: 96 average time/residue: 1.4885 time to fit residues: 148.9499 Evaluate side-chains 104 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 14 LEU Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 GLU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 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 18 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 73 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1291 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= 0.183 Angle : 0.470 5.269 8551 Z= 0.253 Chirality : 0.042 0.165 971 Planarity : 0.003 0.036 1083 Dihedral : 13.175 172.668 946 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % Rotamer: Outliers : 4.09 % Allowed : 22.80 % 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: 1.22 (0.30), residues: 791 helix: 2.10 (0.29), residues: 292 sheet: 0.88 (0.41), residues: 155 loop : -0.33 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.002 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 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.697 Fit side-chains REVERT: A 101 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.7079 (m-80) REVERT: A 117 GLU cc_start: 0.7225 (tp30) cc_final: 0.6988 (tm-30) REVERT: A 212 MET cc_start: 0.7866 (mtm) cc_final: 0.7319 (mmm) REVERT: A 217 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: A 229 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7210 (mt0) REVERT: F 27 MET cc_start: 0.7877 (ptm) cc_final: 0.7576 (ptm) REVERT: F 102 ILE cc_start: 0.8662 (mm) cc_final: 0.8439 (mp) REVERT: F 111 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7973 (pt) REVERT: F 184 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7328 (tm-30) REVERT: F 197 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8038 (ppp) REVERT: F 226 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8311 (mtt-85) REVERT: F 271 TYR cc_start: 0.7866 (m-10) cc_final: 0.7567 (m-80) REVERT: G 183 LYS cc_start: 0.8450 (tppp) cc_final: 0.7805 (tptp) outliers start: 26 outliers final: 12 residues processed: 100 average time/residue: 1.4179 time to fit residues: 148.1171 Evaluate side-chains 101 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 A residue 229 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1386 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= 0.402 Angle : 0.615 5.853 8551 Z= 0.319 Chirality : 0.048 0.269 971 Planarity : 0.005 0.048 1083 Dihedral : 13.916 173.800 946 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.60 % Rotamer: Outliers : 4.09 % Allowed : 21.86 % 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: 0.80 (0.29), residues: 791 helix: 1.73 (0.29), residues: 280 sheet: 0.79 (0.42), residues: 144 loop : -0.51 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 129 HIS 0.003 0.001 HIS F 163 PHE 0.016 0.002 PHE G 203 TYR 0.006 0.002 TYR A 103 ARG 0.006 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 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 101 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: A 131 SER cc_start: 0.7778 (OUTLIER) cc_final: 0.7470 (m) REVERT: A 212 MET cc_start: 0.7853 (mtm) cc_final: 0.7359 (mmm) REVERT: A 229 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7567 (mt0) REVERT: F 27 MET cc_start: 0.7965 (ptm) cc_final: 0.7700 (ptm) REVERT: F 111 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7988 (pt) REVERT: F 226 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8406 (mtt-85) REVERT: F 271 TYR cc_start: 0.7881 (m-10) cc_final: 0.7586 (m-80) REVERT: G 120 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: G 332 ASN cc_start: 0.0688 (OUTLIER) cc_final: -0.0175 (p0) outliers start: 26 outliers final: 15 residues processed: 97 average time/residue: 1.4430 time to fit residues: 145.9978 Evaluate side-chains 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 229 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 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 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 14 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6315 Z= 0.325 Angle : 0.566 5.833 8551 Z= 0.298 Chirality : 0.046 0.245 971 Planarity : 0.004 0.040 1083 Dihedral : 14.147 174.078 946 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.02 % Favored : 97.85 % Rotamer: Outliers : 3.93 % Allowed : 22.64 % 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: 0.63 (0.29), residues: 791 helix: 1.59 (0.30), residues: 280 sheet: 0.50 (0.41), residues: 155 loop : -0.53 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 129 HIS 0.003 0.001 HIS F 163 PHE 0.013 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 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 101 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6945 (m-80) REVERT: A 131 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7559 (m) REVERT: A 212 MET cc_start: 0.7858 (mtm) cc_final: 0.7400 (mmm) REVERT: A 229 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: F 27 MET cc_start: 0.7893 (ptm) cc_final: 0.7631 (ptm) REVERT: F 111 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7986 (pt) REVERT: F 226 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8445 (mtt-85) REVERT: F 271 TYR cc_start: 0.7793 (m-10) cc_final: 0.7574 (m-80) REVERT: G 332 ASN cc_start: 0.0163 (OUTLIER) cc_final: -0.0610 (t0) outliers start: 25 outliers final: 13 residues processed: 98 average time/residue: 1.4311 time to fit residues: 146.3284 Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 229 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 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 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 30 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1467 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= 0.179 Angle : 0.482 5.377 8551 Z= 0.259 Chirality : 0.042 0.192 971 Planarity : 0.003 0.036 1083 Dihedral : 13.742 173.375 946 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.26 % Favored : 98.61 % 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: 0.93 (0.30), residues: 791 helix: 1.98 (0.30), residues: 280 sheet: 0.61 (0.41), residues: 155 loop : -0.46 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 F 28 *********************** 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 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.627 Fit side-chains REVERT: A 101 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: A 103 TYR cc_start: 0.8636 (m-80) cc_final: 0.8394 (m-80) REVERT: A 131 SER cc_start: 0.7814 (OUTLIER) cc_final: 0.7572 (m) REVERT: A 193 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8304 (tmmm) REVERT: A 212 MET cc_start: 0.7867 (mtm) cc_final: 0.7393 (mmm) REVERT: A 229 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: F 27 MET cc_start: 0.7862 (ptm) cc_final: 0.7562 (ptm) REVERT: F 111 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8026 (pt) REVERT: F 226 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8287 (mtt-85) REVERT: G 332 ASN cc_start: 0.0053 (OUTLIER) cc_final: -0.0682 (t0) outliers start: 23 outliers final: 10 residues processed: 99 average time/residue: 1.3762 time to fit residues: 142.2073 Evaluate side-chains 99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 229 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 F residue 226 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain G residue 332 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.0060 chunk 66 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 213 ASN G 113 ASN G 118 GLN G 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1537 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= 0.171 Angle : 0.472 6.047 8551 Z= 0.255 Chirality : 0.042 0.181 971 Planarity : 0.003 0.036 1083 Dihedral : 13.426 174.760 946 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.14 % Favored : 98.74 % Rotamer: Outliers : 2.67 % Allowed : 23.90 % 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: 1.06 (0.30), residues: 791 helix: 2.01 (0.30), residues: 292 sheet: 0.74 (0.41), residues: 155 loop : -0.44 (0.34), residues: 344 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 260 TYR 0.007 0.001 TYR F 103 ARG 0.002 0.000 ARG G 169 ********************** 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: 17 poor density : 80 time to evaluate : 0.698 Fit side-chains REVERT: A 101 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: A 103 TYR cc_start: 0.8647 (m-80) cc_final: 0.8429 (m-80) REVERT: A 131 SER cc_start: 0.7809 (OUTLIER) cc_final: 0.7579 (m) REVERT: A 193 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8314 (tmmm) REVERT: A 229 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7402 (mt0) REVERT: F 27 MET cc_start: 0.7824 (ptm) cc_final: 0.7508 (ptm) REVERT: F 111 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8025 (pt) REVERT: F 197 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8234 (ppp) REVERT: F 226 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8270 (mtt-85) REVERT: G 332 ASN cc_start: 0.0077 (OUTLIER) cc_final: -0.0644 (t0) outliers start: 17 outliers final: 6 residues processed: 91 average time/residue: 1.4025 time to fit residues: 133.1954 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 : 0.804 ------------------------------------------------------------------------------- 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 229 GLN Chi-restraints excluded: chain F residue 14 LEU 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 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 17 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 45 optimal weight: 0.0070 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 213 ASN ** G 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.157809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.122677 restraints weight = 6209.497| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.20 r_work: 0.2887 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 6315 Z= 0.372 Angle : 0.611 8.239 8551 Z= 0.316 Chirality : 0.047 0.288 971 Planarity : 0.005 0.045 1083 Dihedral : 13.821 173.095 943 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.60 % 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: 0.71 (0.29), residues: 791 helix: 1.75 (0.30), residues: 280 sheet: 0.48 (0.40), residues: 155 loop : -0.55 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 129 HIS 0.004 0.001 HIS F 163 PHE 0.014 0.002 PHE G 203 TYR 0.010 0.001 TYR F 271 ARG 0.004 0.001 ARG F 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2639.47 seconds wall clock time: 48 minutes 20.67 seconds (2900.67 seconds total)