Starting phenix.real_space_refine on Thu Jan 16 23:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjr_39347/01_2025/8yjr_39347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjr_39347/01_2025/8yjr_39347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjr_39347/01_2025/8yjr_39347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjr_39347/01_2025/8yjr_39347.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjr_39347/01_2025/8yjr_39347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjr_39347/01_2025/8yjr_39347.cif" } resolution = 3.51 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 263 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 61 5.16 5 C 6072 2.51 5 N 1671 2.21 5 O 2093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9962 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1963 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "D" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2774 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "A" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 228 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 6.47, per 1000 atoms: 0.65 Number of scatterers: 9962 At special positions: 0 Unit cell: (106.24, 102.92, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 P 65 15.00 O 2093 8.00 N 1671 7.00 C 6072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 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: 2.46 Conformation dependent library (CDL) restraints added in 984.4 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 29.3% alpha, 24.9% beta 10 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.457A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 22 through 26 removed outlier: 3.972A pdb=" N TYR D 26 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 46 removed outlier: 3.737A pdb=" N ILE D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 46 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.682A pdb=" N MET D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 116 removed outlier: 4.009A pdb=" N ALA D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 130 Processing helix chain 'D' and resid 134 through 148 removed outlier: 3.569A pdb=" N ASN D 138 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 230 removed outlier: 3.678A pdb=" N ASP D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 253 Processing helix chain 'D' and resid 255 through 262 removed outlier: 3.570A pdb=" N ILE D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 333 removed outlier: 3.632A pdb=" N GLN D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.566A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.617A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 196 " --> pdb=" O LYS B 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 208 removed outlier: 5.513A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 167 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 179 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 71 removed outlier: 6.783A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 123 through 127 removed outlier: 5.825A pdb=" N GLY C 127 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL D 346 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 208 removed outlier: 5.088A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 167 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.254A pdb=" N ALA D 175 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS D 30 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA D 176 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA D 32 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 31 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 84 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE D 33 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.521A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 251 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2562 1.33 - 1.45: 2028 1.45 - 1.58: 5430 1.58 - 1.70: 126 1.70 - 1.82: 98 Bond restraints: 10244 Sorted by residual: bond pdb=" C3' DT E 0 " pdb=" O3' DT E 0 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.45e+00 bond pdb=" CB ASN A 177 " pdb=" CG ASN A 177 " ideal model delta sigma weight residual 1.516 1.568 -0.052 2.50e-02 1.60e+03 4.41e+00 bond pdb=" C3' DA E 14 " pdb=" O3' DA E 14 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 4.04e+00 bond pdb=" C3' DA J 15 " pdb=" O3' DA J 15 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.86e+00 bond pdb=" CB GLU B 191 " pdb=" CG GLU B 191 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.78e+00 ... (remaining 10239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 13811 2.93 - 5.86: 246 5.86 - 8.79: 32 8.79 - 11.72: 8 11.72 - 14.65: 1 Bond angle restraints: 14098 Sorted by residual: angle pdb=" C ALA A 242 " pdb=" N ASP A 243 " pdb=" CA ASP A 243 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C ALA B 242 " pdb=" N ASP B 243 " pdb=" CA ASP B 243 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N THR B 219 " pdb=" CA THR B 219 " pdb=" C THR B 219 " ideal model delta sigma weight residual 109.81 120.02 -10.21 2.21e+00 2.05e-01 2.14e+01 angle pdb=" C ALA C 231 " pdb=" N ASP C 232 " pdb=" CA ASP C 232 " ideal model delta sigma weight residual 121.54 129.93 -8.39 1.91e+00 2.74e-01 1.93e+01 angle pdb=" CA LEU D 130 " pdb=" CB LEU D 130 " pdb=" CG LEU D 130 " ideal model delta sigma weight residual 116.30 130.95 -14.65 3.50e+00 8.16e-02 1.75e+01 ... (remaining 14093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 5762 35.17 - 70.34: 408 70.34 - 105.51: 16 105.51 - 140.68: 1 140.68 - 175.85: 2 Dihedral angle restraints: 6189 sinusoidal: 2949 harmonic: 3240 Sorted by residual: dihedral pdb=" C4' DT E 0 " pdb=" C3' DT E 0 " pdb=" O3' DT E 0 " pdb=" P DT E 1 " ideal model delta sinusoidal sigma weight residual -140.00 35.85 -175.85 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA THR B 216 " pdb=" C THR B 216 " pdb=" N LYS B 217 " pdb=" CA LYS B 217 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C4' DA E 14 " pdb=" C3' DA E 14 " pdb=" O3' DA E 14 " pdb=" P DA E 15 " ideal model delta sinusoidal sigma weight residual -140.00 4.42 -144.42 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 6186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1249 0.054 - 0.108: 272 0.108 - 0.162: 82 0.162 - 0.216: 15 0.216 - 0.270: 5 Chirality restraints: 1623 Sorted by residual: chirality pdb=" CB ILE A 128 " pdb=" CA ILE A 128 " pdb=" CG1 ILE A 128 " pdb=" CG2 ILE A 128 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" P DA E 15 " pdb=" OP1 DA E 15 " pdb=" OP2 DA E 15 " pdb=" O5' DA E 15 " both_signs ideal model delta sigma weight residual True 2.35 -2.60 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL A 45 " pdb=" CA VAL A 45 " pdb=" CG1 VAL A 45 " pdb=" CG2 VAL A 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1620 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 219 " 0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO B 220 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.052 5.00e-02 4.00e+02 7.79e-02 9.72e+00 pdb=" N PRO A 220 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 233 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.31e+00 pdb=" N PRO B 234 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " 0.037 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2889 2.84 - 3.36: 8152 3.36 - 3.87: 17979 3.87 - 4.39: 19717 4.39 - 4.90: 33111 Nonbonded interactions: 81848 Sorted by model distance: nonbonded pdb=" O VAL D 123 " pdb=" OG1 THR D 127 " model vdw 2.330 3.040 nonbonded pdb=" OG SER A 43 " pdb=" OH TYR A 211 " model vdw 2.372 3.040 nonbonded pdb=" OG SER C 43 " pdb=" OH TYR C 211 " model vdw 2.375 3.040 nonbonded pdb=" OD2 ASP C 41 " pdb=" OG SER C 43 " model vdw 2.376 3.040 nonbonded pdb=" OG SER B 141 " pdb=" O SER B 222 " model vdw 2.390 3.040 ... (remaining 81843 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 'A' selection = chain 'B' selection = (chain 'C' and resid 2 through 254) } 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 group one per residue 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.710 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.005 0.070 10244 Z= 0.300 Angle : 0.943 14.649 14098 Z= 0.494 Chirality : 0.053 0.270 1623 Planarity : 0.007 0.085 1593 Dihedral : 20.532 175.855 4078 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.40 (0.21), residues: 1105 helix: -2.95 (0.19), residues: 314 sheet: -1.36 (0.30), residues: 290 loop : -2.22 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 28 HIS 0.005 0.001 HIS D 280 PHE 0.028 0.002 PHE D 283 TYR 0.024 0.003 TYR D 69 ARG 0.006 0.001 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 MET cc_start: 0.6419 (tpt) cc_final: 0.5938 (ppp) REVERT: D 325 VAL cc_start: 0.8445 (t) cc_final: 0.7941 (m) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2124 time to fit residues: 44.1851 Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 36 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 GLN D 273 ASN A 38 GLN A 204 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.130350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100048 restraints weight = 16968.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.103432 restraints weight = 12713.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103706 restraints weight = 7733.325| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10244 Z= 0.243 Angle : 0.628 7.505 14098 Z= 0.348 Chirality : 0.044 0.167 1623 Planarity : 0.005 0.059 1593 Dihedral : 21.899 178.294 1944 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.93 % Allowed : 9.73 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.32 (0.22), residues: 1105 helix: -1.18 (0.25), residues: 326 sheet: -1.27 (0.27), residues: 326 loop : -1.86 (0.24), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 28 HIS 0.002 0.001 HIS D 276 PHE 0.012 0.001 PHE D 126 TYR 0.017 0.002 TYR A 250 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.7889 (mmm) cc_final: 0.7674 (mmt) REVERT: D 65 MET cc_start: 0.6841 (tpt) cc_final: 0.6592 (ppp) REVERT: D 191 MET cc_start: 0.8214 (mtm) cc_final: 0.7848 (mtm) outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.2066 time to fit residues: 35.0696 Evaluate side-chains 97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN D 77 ASN D 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.130535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.100274 restraints weight = 17247.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103748 restraints weight = 12336.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104585 restraints weight = 7402.975| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10244 Z= 0.182 Angle : 0.559 6.825 14098 Z= 0.307 Chirality : 0.042 0.144 1623 Planarity : 0.004 0.050 1593 Dihedral : 21.898 176.313 1944 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.24 % Allowed : 12.32 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.72 (0.23), residues: 1105 helix: -0.21 (0.28), residues: 326 sheet: -1.12 (0.27), residues: 338 loop : -1.72 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 298 HIS 0.001 0.000 HIS A 246 PHE 0.022 0.001 PHE D 68 TYR 0.013 0.001 TYR A 211 ARG 0.002 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.7828 (mmm) cc_final: 0.7617 (mmt) REVERT: D 65 MET cc_start: 0.6975 (tpt) cc_final: 0.6640 (ppp) REVERT: D 152 TYR cc_start: 0.7637 (p90) cc_final: 0.7418 (p90) outliers start: 12 outliers final: 7 residues processed: 113 average time/residue: 0.2130 time to fit residues: 34.9395 Evaluate side-chains 97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 0.0980 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.126595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096119 restraints weight = 17132.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099637 restraints weight = 12766.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.099864 restraints weight = 7679.351| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10244 Z= 0.262 Angle : 0.600 9.118 14098 Z= 0.324 Chirality : 0.044 0.194 1623 Planarity : 0.004 0.045 1593 Dihedral : 21.931 177.108 1944 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.55 % Allowed : 13.77 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.24), residues: 1105 helix: 0.29 (0.29), residues: 326 sheet: -1.24 (0.26), residues: 349 loop : -1.38 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 28 HIS 0.002 0.001 HIS A 246 PHE 0.014 0.002 PHE D 68 TYR 0.014 0.002 TYR A 211 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: D 65 MET cc_start: 0.7064 (tpt) cc_final: 0.6863 (ppp) REVERT: D 152 TYR cc_start: 0.8042 (p90) cc_final: 0.7841 (p90) REVERT: A 75 MET cc_start: 0.8420 (ttt) cc_final: 0.8184 (ttt) outliers start: 15 outliers final: 5 residues processed: 105 average time/residue: 0.2024 time to fit residues: 31.3220 Evaluate side-chains 90 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 0.0370 chunk 93 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.128491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098140 restraints weight = 16932.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.101425 restraints weight = 12695.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101849 restraints weight = 7759.334| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10244 Z= 0.188 Angle : 0.553 8.362 14098 Z= 0.300 Chirality : 0.042 0.169 1623 Planarity : 0.003 0.040 1593 Dihedral : 21.795 176.963 1944 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.76 % Allowed : 14.60 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.24), residues: 1105 helix: 0.53 (0.29), residues: 328 sheet: -1.23 (0.26), residues: 355 loop : -1.25 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 298 HIS 0.001 0.000 HIS A 246 PHE 0.012 0.001 PHE D 68 TYR 0.014 0.001 TYR B 249 ARG 0.002 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 MET cc_start: 0.7027 (tpt) cc_final: 0.6818 (ppp) REVERT: A 75 MET cc_start: 0.8502 (ttt) cc_final: 0.8230 (ttt) outliers start: 17 outliers final: 8 residues processed: 119 average time/residue: 0.1879 time to fit residues: 33.4299 Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.126823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.096294 restraints weight = 17021.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099679 restraints weight = 12937.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.100005 restraints weight = 7789.559| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10244 Z= 0.247 Angle : 0.588 9.287 14098 Z= 0.314 Chirality : 0.043 0.220 1623 Planarity : 0.003 0.034 1593 Dihedral : 21.748 177.160 1944 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.97 % Allowed : 16.05 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.25), residues: 1105 helix: 0.71 (0.30), residues: 329 sheet: -1.22 (0.26), residues: 349 loop : -1.15 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 298 HIS 0.002 0.001 HIS D 193 PHE 0.013 0.001 PHE D 68 TYR 0.013 0.002 TYR B 249 ARG 0.003 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: D 110 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7688 (mp10) REVERT: D 339 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7411 (mpt90) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.2037 time to fit residues: 31.9382 Evaluate side-chains 101 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.126221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095499 restraints weight = 17295.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098369 restraints weight = 13491.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.098918 restraints weight = 8280.052| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10244 Z= 0.254 Angle : 0.602 8.387 14098 Z= 0.321 Chirality : 0.043 0.200 1623 Planarity : 0.003 0.034 1593 Dihedral : 21.695 177.229 1944 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.69 % Allowed : 15.73 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.25), residues: 1105 helix: 0.77 (0.30), residues: 327 sheet: -1.27 (0.26), residues: 348 loop : -1.06 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 298 HIS 0.002 0.000 HIS D 193 PHE 0.013 0.001 PHE A 207 TYR 0.013 0.002 TYR A 211 ARG 0.003 0.000 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 1.054 Fit side-chains REVERT: D 110 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: D 339 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7524 (mpt90) outliers start: 26 outliers final: 11 residues processed: 109 average time/residue: 0.1932 time to fit residues: 31.2797 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.0870 chunk 77 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN C 24 ASN D 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.128355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097861 restraints weight = 17124.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.100730 restraints weight = 12479.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.101137 restraints weight = 8122.246| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10244 Z= 0.190 Angle : 0.594 10.802 14098 Z= 0.313 Chirality : 0.042 0.187 1623 Planarity : 0.003 0.036 1593 Dihedral : 21.599 177.100 1944 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.35 % Allowed : 17.08 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.25), residues: 1105 helix: 0.97 (0.30), residues: 324 sheet: -1.25 (0.26), residues: 348 loop : -1.04 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 298 HIS 0.001 0.000 HIS A 246 PHE 0.014 0.001 PHE D 68 TYR 0.012 0.001 TYR B 249 ARG 0.002 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.015 Fit side-chains REVERT: C 40 MET cc_start: 0.7966 (ttm) cc_final: 0.7730 (ttm) REVERT: D 110 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: D 178 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7235 (mm-30) REVERT: D 339 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7557 (mpt90) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.2196 time to fit residues: 34.7076 Evaluate side-chains 97 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN D 273 ASN A 187 ASN ** A 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092594 restraints weight = 17066.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.095378 restraints weight = 10601.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096941 restraints weight = 7769.210| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10244 Z= 0.336 Angle : 0.667 10.174 14098 Z= 0.349 Chirality : 0.044 0.193 1623 Planarity : 0.003 0.034 1593 Dihedral : 21.651 177.401 1944 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.07 % Allowed : 16.67 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.25), residues: 1105 helix: 0.86 (0.30), residues: 326 sheet: -1.37 (0.26), residues: 348 loop : -1.07 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 28 HIS 0.003 0.001 HIS D 193 PHE 0.014 0.002 PHE A 207 TYR 0.016 0.002 TYR A 211 ARG 0.004 0.000 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.009 Fit side-chains REVERT: D 110 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: D 339 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7710 (mpt90) REVERT: A 19 LEU cc_start: 0.9140 (mp) cc_final: 0.8922 (mt) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.2091 time to fit residues: 31.7377 Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092860 restraints weight = 17110.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095711 restraints weight = 10500.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097678 restraints weight = 7608.416| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 10244 Z= 0.339 Angle : 0.909 59.194 14098 Z= 0.531 Chirality : 0.045 0.414 1623 Planarity : 0.004 0.056 1593 Dihedral : 21.653 177.414 1944 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.86 % Allowed : 17.18 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1105 helix: 0.88 (0.30), residues: 326 sheet: -1.38 (0.26), residues: 348 loop : -1.10 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 28 HIS 0.002 0.001 HIS D 193 PHE 0.015 0.002 PHE D 185 TYR 0.015 0.002 TYR A 211 ARG 0.004 0.000 ARG D 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.058 Fit side-chains REVERT: D 110 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: D 339 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.7706 (mpt90) REVERT: A 19 LEU cc_start: 0.9138 (mp) cc_final: 0.8919 (mt) outliers start: 18 outliers final: 15 residues processed: 97 average time/residue: 0.2149 time to fit residues: 30.6843 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 205 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.092840 restraints weight = 17086.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095706 restraints weight = 10488.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.097698 restraints weight = 7612.933| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 10244 Z= 0.339 Angle : 0.909 59.194 14098 Z= 0.531 Chirality : 0.045 0.414 1623 Planarity : 0.004 0.056 1593 Dihedral : 21.653 177.414 1944 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.76 % Allowed : 17.29 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1105 helix: 0.88 (0.30), residues: 326 sheet: -1.38 (0.26), residues: 348 loop : -1.10 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 28 HIS 0.002 0.001 HIS D 193 PHE 0.015 0.002 PHE D 185 TYR 0.015 0.002 TYR A 211 ARG 0.004 0.000 ARG D 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2715.09 seconds wall clock time: 50 minutes 11.71 seconds (3011.71 seconds total)