Starting phenix.real_space_refine on Wed Sep 17 17:36:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjr_39347/09_2025/8yjr_39347.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjr_39347/09_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_39347/09_2025/8yjr_39347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjr_39347/09_2025/8yjr_39347.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjr_39347/09_2025/8yjr_39347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjr_39347/09_2025/8yjr_39347.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.45, per 1000 atoms: 0.25 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: 0.91 Conformation dependent library (CDL) restraints added in 339.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.21 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: 1.85 Time building geometry restraints manager: 1.19 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.600 ------------------------------------------------------------------------------- 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 10247 Z= 0.220 Angle : 0.942 14.649 14104 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.006 0.001 ARG C 146 TYR 0.024 0.003 TYR D 69 PHE 0.028 0.002 PHE D 283 TRP 0.007 0.001 TRP B 28 HIS 0.005 0.001 HIS D 280 Details of bonding type rmsd covalent geometry : bond 0.00483 (10244) covalent geometry : angle 0.94261 (14098) SS BOND : bond 0.00114 ( 3) SS BOND : angle 0.63377 ( 6) hydrogen bonds : bond 0.20670 ( 445) hydrogen bonds : angle 9.85319 ( 1234) *********************** 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 : 0.372 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: 0.0936 time to fit residues: 19.5451 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 : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 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 B 36 ASN D 77 ASN D 220 GLN D 273 ASN A 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.129183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098755 restraints weight = 17047.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.102115 restraints weight = 12819.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102362 restraints weight = 7798.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.102648 restraints weight = 7985.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104737 restraints weight = 7054.776| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10247 Z= 0.196 Angle : 0.637 7.258 14104 Z= 0.354 Chirality : 0.044 0.171 1623 Planarity : 0.005 0.056 1593 Dihedral : 21.884 177.625 1944 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.04 % Allowed : 10.04 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.22), residues: 1105 helix: -1.05 (0.25), residues: 326 sheet: -1.30 (0.28), residues: 319 loop : -1.81 (0.24), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.018 0.002 TYR A 250 PHE 0.020 0.002 PHE D 126 TRP 0.006 0.001 TRP B 28 HIS 0.002 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00441 (10244) covalent geometry : angle 0.63709 (14098) SS BOND : bond 0.00137 ( 3) SS BOND : angle 0.86050 ( 6) hydrogen bonds : bond 0.04342 ( 445) hydrogen bonds : angle 6.51821 ( 1234) *********************** 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 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 37 MET cc_start: 0.7914 (mmm) cc_final: 0.7658 (mmt) REVERT: D 65 MET cc_start: 0.6851 (tpt) cc_final: 0.6533 (ppp) outliers start: 10 outliers final: 5 residues processed: 118 average time/residue: 0.0902 time to fit residues: 15.7238 Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN B 49 GLN D 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.129280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.099027 restraints weight = 17124.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.101782 restraints weight = 13225.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.102386 restraints weight = 8264.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104151 restraints weight = 7810.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.104143 restraints weight = 6795.937| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10247 Z= 0.146 Angle : 0.569 6.828 14104 Z= 0.312 Chirality : 0.042 0.153 1623 Planarity : 0.004 0.049 1593 Dihedral : 21.922 176.174 1944 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.24 % Allowed : 12.42 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.23), residues: 1105 helix: -0.15 (0.28), residues: 326 sheet: -1.23 (0.27), residues: 343 loop : -1.66 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 146 TYR 0.014 0.001 TYR A 211 PHE 0.022 0.001 PHE D 68 TRP 0.004 0.001 TRP D 298 HIS 0.001 0.000 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00328 (10244) covalent geometry : angle 0.56884 (14098) SS BOND : bond 0.00253 ( 3) SS BOND : angle 0.72039 ( 6) hydrogen bonds : bond 0.03492 ( 445) hydrogen bonds : angle 6.00454 ( 1234) *********************** 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 : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: B 75 MET cc_start: 0.9036 (tmm) cc_final: 0.8571 (ttt) REVERT: D 65 MET cc_start: 0.6984 (tpt) cc_final: 0.6667 (ppp) REVERT: D 152 TYR cc_start: 0.7737 (p90) cc_final: 0.7519 (p90) outliers start: 12 outliers final: 6 residues processed: 114 average time/residue: 0.0958 time to fit residues: 15.8767 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 GLN 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 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 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.126772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096103 restraints weight = 17233.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098427 restraints weight = 14138.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099440 restraints weight = 8892.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.100285 restraints weight = 7798.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.100520 restraints weight = 7370.271| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10247 Z= 0.190 Angle : 0.599 8.875 14104 Z= 0.324 Chirality : 0.043 0.161 1623 Planarity : 0.004 0.044 1593 Dihedral : 21.945 176.899 1944 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.86 % Allowed : 13.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.24), residues: 1105 helix: 0.25 (0.29), residues: 326 sheet: -1.22 (0.26), residues: 353 loop : -1.38 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 61 TYR 0.015 0.002 TYR A 211 PHE 0.012 0.001 PHE D 68 TRP 0.005 0.001 TRP B 28 HIS 0.002 0.001 HIS B 246 Details of bonding type rmsd covalent geometry : bond 0.00432 (10244) covalent geometry : angle 0.59943 (14098) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.60313 ( 6) hydrogen bonds : bond 0.03598 ( 445) hydrogen bonds : angle 5.87798 ( 1234) *********************** 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 111 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8798 (ttt) REVERT: D 65 MET cc_start: 0.7082 (tpt) cc_final: 0.6859 (ppp) REVERT: D 110 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7798 (mp10) outliers start: 18 outliers final: 6 residues processed: 105 average time/residue: 0.0870 time to fit residues: 13.6231 Evaluate side-chains 93 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET 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 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 9 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.0170 chunk 84 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.127865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097481 restraints weight = 17074.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.100376 restraints weight = 13265.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.100985 restraints weight = 8201.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101833 restraints weight = 7677.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.101962 restraints weight = 7165.139| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10247 Z= 0.142 Angle : 0.563 8.351 14104 Z= 0.305 Chirality : 0.042 0.156 1623 Planarity : 0.003 0.040 1593 Dihedral : 21.832 176.877 1944 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.76 % Allowed : 14.08 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.24), residues: 1105 helix: 0.50 (0.29), residues: 327 sheet: -1.25 (0.26), residues: 355 loop : -1.25 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.012 0.001 TYR A 211 PHE 0.013 0.001 PHE D 126 TRP 0.005 0.001 TRP D 298 HIS 0.002 0.000 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00321 (10244) covalent geometry : angle 0.56266 (14098) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.51014 ( 6) hydrogen bonds : bond 0.03141 ( 445) hydrogen bonds : angle 5.68820 ( 1234) *********************** 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 : 0.252 Fit side-chains revert: symmetry clash REVERT: B 75 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8393 (ttt) REVERT: C 12 LEU cc_start: 0.9335 (tp) cc_final: 0.9127 (tp) REVERT: D 65 MET cc_start: 0.7024 (tpt) cc_final: 0.6812 (ppp) REVERT: D 75 MET cc_start: 0.8588 (mmm) cc_final: 0.8386 (mmm) outliers start: 17 outliers final: 10 residues processed: 117 average time/residue: 0.0891 time to fit residues: 15.4391 Evaluate side-chains 101 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET 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 148 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.126719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095180 restraints weight = 17105.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.098290 restraints weight = 12025.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.098772 restraints weight = 8988.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099917 restraints weight = 7230.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100003 restraints weight = 6685.693| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10247 Z= 0.168 Angle : 0.581 8.413 14104 Z= 0.313 Chirality : 0.043 0.246 1623 Planarity : 0.003 0.035 1593 Dihedral : 21.772 177.076 1944 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.07 % Allowed : 16.05 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.25), residues: 1105 helix: 0.64 (0.30), residues: 328 sheet: -1.25 (0.26), residues: 353 loop : -1.20 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.013 0.001 TYR A 211 PHE 0.013 0.001 PHE D 68 TRP 0.004 0.001 TRP D 298 HIS 0.002 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00387 (10244) covalent geometry : angle 0.58121 (14098) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.57034 ( 6) hydrogen bonds : bond 0.03249 ( 445) hydrogen bonds : angle 5.62115 ( 1234) *********************** 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 114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.379 Fit side-chains REVERT: B 75 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8437 (ttt) REVERT: C 199 MET cc_start: 0.7970 (tmm) cc_final: 0.7678 (tmm) REVERT: D 65 MET cc_start: 0.7034 (tpt) cc_final: 0.6816 (ppp) REVERT: D 75 MET cc_start: 0.8655 (mmm) cc_final: 0.8388 (mmm) REVERT: D 339 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7527 (mpt90) outliers start: 20 outliers final: 12 residues processed: 106 average time/residue: 0.0921 time to fit residues: 14.4748 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET 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 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 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 Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 206 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.128183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096879 restraints weight = 17182.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.100631 restraints weight = 11999.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.101166 restraints weight = 7908.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101840 restraints weight = 6576.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102039 restraints weight = 6424.650| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10247 Z= 0.132 Angle : 0.573 10.667 14104 Z= 0.307 Chirality : 0.042 0.167 1623 Planarity : 0.003 0.036 1593 Dihedral : 21.686 176.991 1944 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.25), residues: 1105 helix: 0.81 (0.30), residues: 327 sheet: -1.13 (0.26), residues: 351 loop : -1.13 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 146 TYR 0.011 0.001 TYR A 211 PHE 0.014 0.001 PHE D 68 TRP 0.004 0.001 TRP D 298 HIS 0.001 0.000 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00301 (10244) covalent geometry : angle 0.57314 (14098) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.47306 ( 6) hydrogen bonds : bond 0.02969 ( 445) hydrogen bonds : angle 5.46852 ( 1234) *********************** 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 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.379 Fit side-chains REVERT: B 75 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8412 (ttt) REVERT: D 65 MET cc_start: 0.7037 (tpt) cc_final: 0.6793 (ppp) REVERT: D 75 MET cc_start: 0.8655 (mmm) cc_final: 0.8380 (mmm) REVERT: D 339 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7489 (mpt90) outliers start: 19 outliers final: 9 residues processed: 115 average time/residue: 0.0914 time to fit residues: 15.3195 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET 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 82 VAL 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 Chi-restraints excluded: chain A residue 206 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.126401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.094797 restraints weight = 16970.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098149 restraints weight = 12070.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098663 restraints weight = 8307.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099631 restraints weight = 6915.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099795 restraints weight = 6625.446| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10247 Z= 0.172 Angle : 0.619 9.988 14104 Z= 0.326 Chirality : 0.043 0.185 1623 Planarity : 0.003 0.035 1593 Dihedral : 21.640 177.228 1944 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.55 % Allowed : 17.39 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.25), residues: 1105 helix: 0.90 (0.30), residues: 325 sheet: -1.20 (0.26), residues: 351 loop : -1.07 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 339 TYR 0.014 0.002 TYR A 211 PHE 0.015 0.001 PHE D 185 TRP 0.004 0.001 TRP D 298 HIS 0.002 0.000 HIS D 280 Details of bonding type rmsd covalent geometry : bond 0.00396 (10244) covalent geometry : angle 0.61853 (14098) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.57102 ( 6) hydrogen bonds : bond 0.03232 ( 445) hydrogen bonds : angle 5.47871 ( 1234) *********************** 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 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.382 Fit side-chains REVERT: B 75 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8460 (ttt) REVERT: D 75 MET cc_start: 0.8695 (mmm) cc_final: 0.8370 (mmm) REVERT: D 204 ILE cc_start: 0.8640 (mm) cc_final: 0.8438 (mm) REVERT: D 339 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7738 (mpt90) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.0941 time to fit residues: 13.7430 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET 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 82 VAL 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 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 206 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 273 ASN A 131 GLN A 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.123684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092591 restraints weight = 17044.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094926 restraints weight = 14288.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096739 restraints weight = 8835.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096746 restraints weight = 7449.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097022 restraints weight = 7157.982| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10247 Z= 0.240 Angle : 0.670 10.667 14104 Z= 0.352 Chirality : 0.045 0.197 1623 Planarity : 0.003 0.034 1593 Dihedral : 21.678 177.448 1944 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.66 % Allowed : 17.81 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.25), residues: 1105 helix: 0.76 (0.30), residues: 326 sheet: -1.35 (0.26), residues: 348 loop : -1.10 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.018 0.002 TYR D 40 PHE 0.013 0.002 PHE D 185 TRP 0.009 0.002 TRP D 274 HIS 0.002 0.001 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00553 (10244) covalent geometry : angle 0.67035 (14098) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.65272 ( 6) hydrogen bonds : bond 0.03596 ( 445) hydrogen bonds : angle 5.71561 ( 1234) *********************** 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 103 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.372 Fit side-chains REVERT: B 75 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8511 (ttt) REVERT: D 339 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8207 (mpt90) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.0935 time to fit residues: 13.4049 Evaluate side-chains 96 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET 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 148 MET Chi-restraints excluded: chain D residue 273 ASN 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 Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 55 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 53 optimal weight: 0.2980 chunk 114 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN D 273 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.126891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.095743 restraints weight = 16865.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.098945 restraints weight = 12891.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099722 restraints weight = 7905.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.100069 restraints weight = 7081.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100333 restraints weight = 6774.463| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10247 Z= 0.138 Angle : 0.612 10.191 14104 Z= 0.322 Chirality : 0.043 0.196 1623 Planarity : 0.003 0.037 1593 Dihedral : 21.558 177.166 1944 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.45 % Allowed : 18.32 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.25), residues: 1105 helix: 0.93 (0.30), residues: 325 sheet: -1.28 (0.27), residues: 338 loop : -1.06 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.017 0.002 TYR D 40 PHE 0.014 0.001 PHE D 68 TRP 0.022 0.002 TRP D 274 HIS 0.002 0.000 HIS D 276 Details of bonding type rmsd covalent geometry : bond 0.00317 (10244) covalent geometry : angle 0.61171 (14098) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.50195 ( 6) hydrogen bonds : bond 0.03019 ( 445) hydrogen bonds : angle 5.49526 ( 1234) ********************** 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 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.420 Fit side-chains REVERT: B 75 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8441 (ttt) REVERT: D 339 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7706 (mpt90) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.0924 time to fit residues: 13.7963 Evaluate side-chains 98 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 MET 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 148 MET Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 206 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.125659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094010 restraints weight = 17126.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096460 restraints weight = 13473.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097496 restraints weight = 8658.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098153 restraints weight = 7990.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098560 restraints weight = 7162.703| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10247 Z= 0.175 Angle : 0.631 10.564 14104 Z= 0.330 Chirality : 0.043 0.192 1623 Planarity : 0.003 0.035 1593 Dihedral : 21.543 177.208 1944 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.45 % Allowed : 18.22 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.25), residues: 1105 helix: 0.94 (0.29), residues: 328 sheet: -1.30 (0.26), residues: 342 loop : -1.07 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 146 TYR 0.019 0.002 TYR D 40 PHE 0.012 0.001 PHE D 68 TRP 0.006 0.001 TRP D 298 HIS 0.002 0.000 HIS D 193 Details of bonding type rmsd covalent geometry : bond 0.00406 (10244) covalent geometry : angle 0.63131 (14098) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.53829 ( 6) hydrogen bonds : bond 0.03232 ( 445) hydrogen bonds : angle 5.52830 ( 1234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1543.01 seconds wall clock time: 27 minutes 33.28 seconds (1653.28 seconds total)