Starting phenix.real_space_refine on Thu Jul 2 12:25:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyz_60584/07_2026/8zyz_60584.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyz_60584/07_2026/8zyz_60584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zyz_60584/07_2026/8zyz_60584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyz_60584/07_2026/8zyz_60584.map" model { file = "/net/cci-nas-00/data/ceres_data/8zyz_60584/07_2026/8zyz_60584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyz_60584/07_2026/8zyz_60584.cif" } resolution = 3.16 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 78 5.16 5 Na 2 4.78 5 C 5745 2.51 5 N 1471 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 361 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 368 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "C" Number of atoms: 1606 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 bond proxies already assigned to first conformer: 1616 Chain: "D" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1621 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 1 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1729 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1613 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.19 Number of scatterers: 8918 At special positions: 0 Unit cell: (102.6, 98.55, 106.65, 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 78 16.00 Na 2 11.00 O 1622 8.00 N 1471 7.00 C 5745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 362.9 milliseconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 91.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.820A pdb=" N GLY A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 59 Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.943A pdb=" N PHE B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 Processing helix chain 'C' and resid 31 through 50 Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.548A pdb=" N PHE C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.512A pdb=" N ASP C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 168 removed outlier: 3.500A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 174 through 195 removed outlier: 3.623A pdb=" N ALA C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET C 179 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 228 Processing helix chain 'C' and resid 230 through 240 Processing helix chain 'C' and resid 241 through 244 removed outlier: 3.609A pdb=" N GLU C 244 " --> pdb=" O TYR C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 51 through 68 Processing helix chain 'D' and resid 72 through 85 removed outlier: 3.989A pdb=" N ASP D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 115 Processing helix chain 'D' and resid 117 through 167 Proline residue: D 151 - end of helix Processing helix chain 'D' and resid 175 through 196 removed outlier: 3.771A pdb=" N VAL D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 228 Processing helix chain 'D' and resid 230 through 239 removed outlier: 4.067A pdb=" N ILE D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.523A pdb=" N ARG D 247 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 249 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 50 removed outlier: 3.795A pdb=" N ASP E 31 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET E 48 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS E 49 " --> pdb=" O VAL E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 68 Processing helix chain 'E' and resid 72 through 87 Processing helix chain 'E' and resid 102 through 114 Processing helix chain 'E' and resid 117 through 168 Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 171 through 196 removed outlier: 3.552A pdb=" N ILE E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 176 " --> pdb=" O PRO E 172 " (cutoff:3.500A) Proline residue: E 177 - end of helix Processing helix chain 'E' and resid 196 through 228 Processing helix chain 'E' and resid 230 through 240 Processing helix chain 'E' and resid 241 through 244 Processing helix chain 'F' and resid 4 through 23 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.536A pdb=" N VAL F 38 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 68 Processing helix chain 'F' and resid 72 through 87 Processing helix chain 'F' and resid 102 through 115 Processing helix chain 'F' and resid 117 through 167 Proline residue: F 151 - end of helix Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 174 through 195 removed outlier: 3.734A pdb=" N THR F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 227 Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.700A pdb=" N ARG F 247 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 50 Processing helix chain 'G' and resid 51 through 67 Processing helix chain 'G' and resid 72 through 87 Processing helix chain 'G' and resid 102 through 115 removed outlier: 3.610A pdb=" N ASP G 114 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 169 Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 171 through 196 removed outlier: 3.565A pdb=" N GLY G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) Proline residue: G 177 - end of helix Processing helix chain 'G' and resid 196 through 228 Processing helix chain 'G' and resid 230 through 243 removed outlier: 3.937A pdb=" N ASN G 240 " --> pdb=" O SER G 236 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR G 241 " --> pdb=" O TYR G 237 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.791A pdb=" N ARG G 247 " --> pdb=" O GLU G 244 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 812 hydrogen bonds defined for protein. 2411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2896 1.34 - 1.46: 1892 1.46 - 1.59: 4093 1.59 - 1.71: 0 1.71 - 1.83: 154 Bond restraints: 9035 Sorted by residual: bond pdb=" CB MET C 179 " pdb=" CG MET C 179 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.51e+00 bond pdb=" CB ASN G 243 " pdb=" CG ASN G 243 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 bond pdb=" CB MET D 179 " pdb=" CG MET D 179 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CB THR C 158 " pdb=" CG2 THR C 158 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.30e-01 bond pdb=" CB ILE C 61 " pdb=" CG2 ILE C 61 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.86e-01 ... (remaining 9030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 12099 2.58 - 5.17: 62 5.17 - 7.75: 6 7.75 - 10.34: 1 10.34 - 12.92: 1 Bond angle restraints: 12169 Sorted by residual: angle pdb=" CB MET G 83 " pdb=" CG MET G 83 " pdb=" SD MET G 83 " ideal model delta sigma weight residual 112.70 125.62 -12.92 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CG MET G 83 " pdb=" SD MET G 83 " pdb=" CE MET G 83 " ideal model delta sigma weight residual 100.90 106.34 -5.44 2.20e+00 2.07e-01 6.12e+00 angle pdb=" CB MET F 52 " pdb=" CG MET F 52 " pdb=" SD MET F 52 " ideal model delta sigma weight residual 112.70 120.06 -7.36 3.00e+00 1.11e-01 6.02e+00 angle pdb=" C ASP E 148 " pdb=" N VAL E 149 " pdb=" CA VAL E 149 " ideal model delta sigma weight residual 121.55 118.18 3.37 1.42e+00 4.96e-01 5.63e+00 angle pdb=" CB MET B 30 " pdb=" CG MET B 30 " pdb=" SD MET B 30 " ideal model delta sigma weight residual 112.70 105.71 6.99 3.00e+00 1.11e-01 5.43e+00 ... (remaining 12164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4577 17.90 - 35.79: 655 35.79 - 53.69: 175 53.69 - 71.59: 32 71.59 - 89.48: 11 Dihedral angle restraints: 5450 sinusoidal: 2132 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ASP D 133 " pdb=" CB ASP D 133 " pdb=" CG ASP D 133 " pdb=" OD1 ASP D 133 " ideal model delta sinusoidal sigma weight residual -30.00 -89.40 59.40 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB GLU C 211 " pdb=" CG GLU C 211 " pdb=" CD GLU C 211 " pdb=" OE1 GLU C 211 " ideal model delta sinusoidal sigma weight residual 0.00 -89.48 89.48 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP F 31 " pdb=" CB ASP F 31 " pdb=" CG ASP F 31 " pdb=" OD1 ASP F 31 " ideal model delta sinusoidal sigma weight residual -30.00 -85.55 55.55 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 5447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 909 0.029 - 0.059: 370 0.059 - 0.088: 119 0.088 - 0.118: 44 0.118 - 0.147: 5 Chirality restraints: 1447 Sorted by residual: chirality pdb=" CA ASP E 148 " pdb=" N ASP E 148 " pdb=" C ASP E 148 " pdb=" CB ASP E 148 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ASN G 243 " pdb=" N ASN G 243 " pdb=" C ASN G 243 " pdb=" CB ASN G 243 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA PRO D 151 " pdb=" N PRO D 151 " pdb=" C PRO D 151 " pdb=" CB PRO D 151 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1444 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 243 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C ASN G 243 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN G 243 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU G 244 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 148 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" CG ASP C 148 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP C 148 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP C 148 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 15 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO B 16 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " -0.023 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 50 2.65 - 3.21: 8360 3.21 - 3.77: 14464 3.77 - 4.34: 18178 4.34 - 4.90: 31349 Nonbonded interactions: 72401 Sorted by model distance: nonbonded pdb=" OG1 THR E 158 " pdb=" OG1 THR E 186 " model vdw 2.087 3.040 nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 188 " model vdw 2.146 3.040 nonbonded pdb=" O ASN G 243 " pdb=" ND2 ASN G 243 " model vdw 2.157 3.120 nonbonded pdb=" OD1 ASP E 31 " pdb=" OH TYR E 188 " model vdw 2.166 3.040 nonbonded pdb=" O LEU A 35 " pdb=" OG SER A 38 " model vdw 2.201 3.040 ... (remaining 72396 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' and resid 14 through 59) } ncs_group { reference = (chain 'C' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'D' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'E' and (resid 29 through 154 or resid 156 through 250)) selection = (chain 'F' and (resid 15 through 16 or resid 31 through 154 or resid 156 through \ 250)) selection = (chain 'G' and (resid 29 through 154 or resid 156 through 250)) } 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.004 0.039 9035 Z= 0.152 Angle : 0.530 12.923 12169 Z= 0.271 Chirality : 0.037 0.147 1447 Planarity : 0.004 0.042 1544 Dihedral : 18.051 89.484 3310 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.11 % Allowed : 29.12 % Favored : 70.78 % 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 are not related in a simple way. whole: 3.30 (0.25), residues: 1149 helix: 2.52 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -0.18 (0.54), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 216 TYR 0.008 0.001 TYR D 241 PHE 0.014 0.002 PHE E 143 TRP 0.004 0.002 TRP A 18 HIS 0.004 0.001 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9035) covalent geometry : angle 0.53008 / 0.27 (12169) hydrogen bonds : bond 0.10331 / 6.69 ( 812) hydrogen bonds : angle 4.90308 / 3.59 ( 2411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.233 Fit side-chains REVERT: B 30 MET cc_start: 0.8053 (ttt) cc_final: 0.7768 (ttm) REVERT: E 75 ASP cc_start: 0.8422 (m-30) cc_final: 0.7674 (t70) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.0691 time to fit residues: 12.6526 Evaluate side-chains 127 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 243 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.0040 overall best weight: 0.3610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.4002 r_free = 0.4002 target = 0.186676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139817 restraints weight = 18410.392| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 6.66 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9035 Z= 0.107 Angle : 0.442 7.228 12169 Z= 0.229 Chirality : 0.035 0.109 1447 Planarity : 0.003 0.041 1544 Dihedral : 3.300 13.781 1225 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.64 % Allowed : 27.52 % Favored : 71.84 % 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 are not related in a simple way. whole: 3.97 (0.25), residues: 1149 helix: 2.97 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.21 (0.55), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 216 TYR 0.004 0.001 TYR D 188 PHE 0.016 0.001 PHE A 39 TRP 0.003 0.001 TRP A 18 HIS 0.002 0.000 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 9035) covalent geometry : angle 0.44225 / 0.23 (12169) hydrogen bonds : bond 0.03954 / 2.51 ( 812) hydrogen bonds : angle 3.61021 / 2.66 ( 2411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.301 Fit side-chains REVERT: C 67 MET cc_start: 0.7243 (ptt) cc_final: 0.6803 (ptp) REVERT: C 239 LYS cc_start: 0.7404 (mtpp) cc_final: 0.7199 (mtpp) REVERT: E 75 ASP cc_start: 0.8530 (m-30) cc_final: 0.7636 (t70) REVERT: E 179 MET cc_start: 0.8394 (tpt) cc_final: 0.6973 (tpt) REVERT: F 148 ASP cc_start: 0.7689 (m-30) cc_final: 0.7438 (m-30) REVERT: F 207 ARG cc_start: 0.8355 (tpt-90) cc_final: 0.8110 (tpp80) outliers start: 6 outliers final: 1 residues processed: 133 average time/residue: 0.0644 time to fit residues: 12.8344 Evaluate side-chains 127 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 205 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.184219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133461 restraints weight = 15368.272| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.79 r_work: 0.3107 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9035 Z= 0.128 Angle : 0.457 6.240 12169 Z= 0.237 Chirality : 0.036 0.123 1447 Planarity : 0.004 0.043 1544 Dihedral : 3.348 12.953 1223 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.49 % Allowed : 26.46 % Favored : 72.05 % 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 are not related in a simple way. whole: 3.95 (0.25), residues: 1149 helix: 2.94 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -0.11 (0.56), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 216 TYR 0.005 0.001 TYR D 241 PHE 0.015 0.001 PHE A 39 TRP 0.003 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9035) covalent geometry : angle 0.45694 / 0.24 (12169) hydrogen bonds : bond 0.04145 / 2.63 ( 812) hydrogen bonds : angle 3.52992 / 2.60 ( 2411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.226 Fit side-chains REVERT: C 56 PHE cc_start: 0.7308 (m-10) cc_final: 0.6914 (m-80) REVERT: C 67 MET cc_start: 0.7726 (ptt) cc_final: 0.7186 (ptp) REVERT: C 239 LYS cc_start: 0.7566 (mtpp) cc_final: 0.7282 (mtpp) REVERT: E 75 ASP cc_start: 0.8562 (m-30) cc_final: 0.7572 (t70) REVERT: F 148 ASP cc_start: 0.8639 (m-30) cc_final: 0.8347 (m-30) REVERT: F 207 ARG cc_start: 0.8972 (tpt-90) cc_final: 0.8629 (tpp80) REVERT: G 83 MET cc_start: 0.5021 (mmp) cc_final: 0.4668 (mmm) REVERT: G 135 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7338 (mtp180) outliers start: 14 outliers final: 10 residues processed: 138 average time/residue: 0.0704 time to fit residues: 14.1347 Evaluate side-chains 137 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.184883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133693 restraints weight = 15670.158| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.81 r_work: 0.3117 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9035 Z= 0.115 Angle : 0.435 5.917 12169 Z= 0.227 Chirality : 0.035 0.116 1447 Planarity : 0.003 0.042 1544 Dihedral : 3.304 13.116 1223 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.91 % Allowed : 26.57 % Favored : 71.52 % 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 are not related in a simple way. whole: 4.04 (0.25), residues: 1149 helix: 3.00 (0.16), residues: 1011 sheet: None (None), residues: 0 loop : -0.15 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 216 TYR 0.005 0.001 TYR F 188 PHE 0.019 0.001 PHE F 44 TRP 0.003 0.001 TRP A 18 HIS 0.002 0.001 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 9035) covalent geometry : angle 0.43499 / 0.23 (12169) hydrogen bonds : bond 0.03930 / 2.49 ( 812) hydrogen bonds : angle 3.46643 / 2.56 ( 2411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.209 Fit side-chains REVERT: A 26 MET cc_start: 0.8709 (mmm) cc_final: 0.8499 (mmm) REVERT: B 56 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6707 (m-10) REVERT: C 56 PHE cc_start: 0.7361 (m-10) cc_final: 0.6988 (m-80) REVERT: C 67 MET cc_start: 0.7502 (ptt) cc_final: 0.6920 (ptp) REVERT: C 69 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7361 (ptmm) REVERT: C 239 LYS cc_start: 0.7214 (mtpp) cc_final: 0.6958 (mtpp) REVERT: D 179 MET cc_start: 0.7884 (ttm) cc_final: 0.7634 (ttt) REVERT: E 67 MET cc_start: 0.7528 (mmt) cc_final: 0.7208 (ttm) REVERT: E 75 ASP cc_start: 0.8578 (m-30) cc_final: 0.7580 (t70) REVERT: F 148 ASP cc_start: 0.8645 (m-30) cc_final: 0.8192 (m-30) REVERT: G 83 MET cc_start: 0.4933 (mmp) cc_final: 0.4668 (mmm) outliers start: 18 outliers final: 12 residues processed: 144 average time/residue: 0.0634 time to fit residues: 13.5855 Evaluate side-chains 140 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.181739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132668 restraints weight = 14406.698| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.79 r_work: 0.3082 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9035 Z= 0.159 Angle : 0.497 7.464 12169 Z= 0.258 Chirality : 0.038 0.130 1447 Planarity : 0.004 0.044 1544 Dihedral : 3.466 12.405 1223 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.02 % Allowed : 26.46 % Favored : 71.52 % 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 are not related in a simple way. whole: 3.74 (0.25), residues: 1149 helix: 2.79 (0.16), residues: 1011 sheet: None (None), residues: 0 loop : -0.17 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 216 TYR 0.007 0.001 TYR D 241 PHE 0.022 0.002 PHE A 32 TRP 0.004 0.001 TRP A 18 HIS 0.004 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 9035) covalent geometry : angle 0.49721 / 0.26 (12169) hydrogen bonds : bond 0.04489 / 2.86 ( 812) hydrogen bonds : angle 3.59137 / 2.65 ( 2411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.193 Fit side-chains REVERT: B 56 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: C 56 PHE cc_start: 0.7518 (m-10) cc_final: 0.7094 (m-80) REVERT: C 67 MET cc_start: 0.7696 (ptt) cc_final: 0.7138 (ptp) REVERT: C 239 LYS cc_start: 0.7335 (mtpp) cc_final: 0.7128 (mtpp) REVERT: E 67 MET cc_start: 0.7583 (mmt) cc_final: 0.7222 (ttm) REVERT: G 83 MET cc_start: 0.4974 (mmp) cc_final: 0.4664 (mmm) REVERT: G 135 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7395 (mtp180) outliers start: 19 outliers final: 14 residues processed: 140 average time/residue: 0.0627 time to fit residues: 12.7662 Evaluate side-chains 139 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 0.0000 chunk 47 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.3981 r_free = 0.3981 target = 0.184690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.123065 restraints weight = 11724.270| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.93 r_work: 0.3060 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9035 Z= 0.114 Angle : 0.437 6.797 12169 Z= 0.229 Chirality : 0.035 0.129 1447 Planarity : 0.003 0.042 1544 Dihedral : 3.351 12.962 1223 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.13 % Allowed : 26.57 % Favored : 71.31 % 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 are not related in a simple way. whole: 4.09 (0.25), residues: 1149 helix: 3.03 (0.16), residues: 1011 sheet: None (None), residues: 0 loop : -0.15 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 216 TYR 0.005 0.001 TYR F 188 PHE 0.021 0.001 PHE A 32 TRP 0.003 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9035) covalent geometry : angle 0.43692 / 0.23 (12169) hydrogen bonds : bond 0.03850 / 2.45 ( 812) hydrogen bonds : angle 3.46095 / 2.55 ( 2411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.194 Fit side-chains REVERT: B 56 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6549 (m-10) REVERT: C 56 PHE cc_start: 0.7192 (m-10) cc_final: 0.6863 (m-80) REVERT: C 67 MET cc_start: 0.7243 (ptt) cc_final: 0.6641 (ptp) REVERT: C 69 LYS cc_start: 0.8109 (mttp) cc_final: 0.7275 (ptmm) REVERT: E 75 ASP cc_start: 0.8512 (m-30) cc_final: 0.7484 (t70) REVERT: F 148 ASP cc_start: 0.8348 (m-30) cc_final: 0.7918 (m-30) REVERT: G 83 MET cc_start: 0.4859 (mmp) cc_final: 0.4589 (mmm) REVERT: G 135 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7130 (mtp180) outliers start: 20 outliers final: 12 residues processed: 143 average time/residue: 0.0628 time to fit residues: 13.2202 Evaluate side-chains 140 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.3977 r_free = 0.3977 target = 0.184201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124263 restraints weight = 10722.345| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.96 r_work: 0.3026 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9035 Z= 0.127 Angle : 0.463 10.544 12169 Z= 0.242 Chirality : 0.036 0.128 1447 Planarity : 0.004 0.042 1544 Dihedral : 3.377 12.499 1223 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.91 % Allowed : 26.78 % Favored : 71.31 % 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 are not related in a simple way. whole: 4.05 (0.24), residues: 1149 helix: 3.02 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.15 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 216 TYR 0.005 0.001 TYR F 188 PHE 0.028 0.001 PHE A 32 TRP 0.002 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9035) covalent geometry : angle 0.46337 / 0.24 (12169) hydrogen bonds : bond 0.04004 / 2.55 ( 812) hydrogen bonds : angle 3.49815 / 2.58 ( 2411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.242 Fit side-chains REVERT: B 56 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6536 (m-10) REVERT: C 56 PHE cc_start: 0.7158 (m-10) cc_final: 0.6808 (m-80) REVERT: C 69 LYS cc_start: 0.8081 (mttp) cc_final: 0.7179 (ptmm) REVERT: D 179 MET cc_start: 0.7821 (tpp) cc_final: 0.7471 (ttt) REVERT: E 75 ASP cc_start: 0.8439 (m-30) cc_final: 0.7504 (t70) REVERT: F 148 ASP cc_start: 0.8430 (m-30) cc_final: 0.7974 (m-30) REVERT: G 83 MET cc_start: 0.4878 (mmp) cc_final: 0.4599 (mmm) REVERT: G 135 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7138 (mtp180) outliers start: 18 outliers final: 15 residues processed: 139 average time/residue: 0.0693 time to fit residues: 14.1984 Evaluate side-chains 142 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 135 ARG Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.184968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136033 restraints weight = 14430.674| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.80 r_work: 0.3136 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9035 Z= 0.112 Angle : 0.441 7.077 12169 Z= 0.230 Chirality : 0.036 0.132 1447 Planarity : 0.003 0.042 1544 Dihedral : 3.331 12.950 1223 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.70 % Allowed : 27.21 % Favored : 71.09 % 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 are not related in a simple way. whole: 4.18 (0.24), residues: 1149 helix: 3.11 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.15 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 216 TYR 0.005 0.001 TYR F 188 PHE 0.013 0.001 PHE A 39 TRP 0.003 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9035) covalent geometry : angle 0.44061 / 0.23 (12169) hydrogen bonds : bond 0.03833 / 2.44 ( 812) hydrogen bonds : angle 3.45874 / 2.55 ( 2411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.313 Fit side-chains REVERT: B 56 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: C 56 PHE cc_start: 0.7172 (m-10) cc_final: 0.6913 (m-80) REVERT: C 67 MET cc_start: 0.7304 (ptt) cc_final: 0.6814 (ptp) REVERT: C 69 LYS cc_start: 0.8122 (mttp) cc_final: 0.7389 (ptmm) REVERT: D 179 MET cc_start: 0.7874 (tpp) cc_final: 0.7454 (ttt) REVERT: E 75 ASP cc_start: 0.8492 (m-30) cc_final: 0.7607 (t70) REVERT: F 148 ASP cc_start: 0.8333 (m-30) cc_final: 0.7913 (m-30) REVERT: G 83 MET cc_start: 0.4860 (mmp) cc_final: 0.4652 (mmm) outliers start: 16 outliers final: 14 residues processed: 138 average time/residue: 0.0622 time to fit residues: 12.7685 Evaluate side-chains 139 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.182785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 129)---------------| | r_work = 0.3335 r_free = 0.3335 target = 0.125189 restraints weight = 14545.202| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.69 r_work: 0.3070 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9035 Z= 0.154 Angle : 0.495 8.050 12169 Z= 0.257 Chirality : 0.038 0.140 1447 Planarity : 0.004 0.043 1544 Dihedral : 3.494 13.216 1223 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.02 % Allowed : 27.21 % Favored : 70.78 % 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 are not related in a simple way. whole: 3.80 (0.24), residues: 1149 helix: 2.85 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -0.24 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 216 TYR 0.007 0.001 TYR F 188 PHE 0.028 0.002 PHE A 32 TRP 0.004 0.001 TRP A 18 HIS 0.004 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 9035) covalent geometry : angle 0.49531 / 0.26 (12169) hydrogen bonds : bond 0.04419 / 2.81 ( 812) hydrogen bonds : angle 3.58808 / 2.65 ( 2411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.314 Fit side-chains REVERT: B 56 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.6600 (m-10) REVERT: C 56 PHE cc_start: 0.7450 (m-10) cc_final: 0.7049 (m-80) REVERT: C 67 MET cc_start: 0.7552 (ptt) cc_final: 0.7070 (ptp) REVERT: C 69 LYS cc_start: 0.8063 (mttp) cc_final: 0.7228 (ptmm) REVERT: D 179 MET cc_start: 0.8094 (tpp) cc_final: 0.7601 (ttt) REVERT: E 75 ASP cc_start: 0.8433 (m-30) cc_final: 0.7513 (t70) REVERT: F 148 ASP cc_start: 0.8600 (m-30) cc_final: 0.8119 (m-30) REVERT: G 83 MET cc_start: 0.4929 (mmp) cc_final: 0.4634 (mmm) outliers start: 19 outliers final: 16 residues processed: 143 average time/residue: 0.0635 time to fit residues: 13.4741 Evaluate side-chains 146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.3978 r_free = 0.3978 target = 0.184460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3323 r_free = 0.3323 target = 0.124111 restraints weight = 10380.389| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.83 r_work: 0.3072 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9035 Z= 0.123 Angle : 0.470 10.998 12169 Z= 0.245 Chirality : 0.036 0.143 1447 Planarity : 0.004 0.041 1544 Dihedral : 3.424 13.455 1223 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.81 % Allowed : 26.99 % Favored : 71.20 % 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 are not related in a simple way. whole: 4.00 (0.24), residues: 1149 helix: 2.98 (0.16), residues: 1009 sheet: None (None), residues: 0 loop : -0.23 (0.53), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 216 TYR 0.004 0.001 TYR F 188 PHE 0.037 0.001 PHE A 32 TRP 0.002 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9035) covalent geometry : angle 0.47005 / 0.24 (12169) hydrogen bonds : bond 0.04007 / 2.55 ( 812) hydrogen bonds : angle 3.53052 / 2.61 ( 2411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.326 Fit side-chains REVERT: B 56 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: C 56 PHE cc_start: 0.7234 (m-10) cc_final: 0.6907 (m-80) REVERT: C 67 MET cc_start: 0.7419 (ptt) cc_final: 0.6941 (ptp) REVERT: C 69 LYS cc_start: 0.8038 (mttp) cc_final: 0.7222 (ptmm) REVERT: C 195 MET cc_start: 0.8759 (mmm) cc_final: 0.8458 (mmm) REVERT: D 179 MET cc_start: 0.7705 (tpp) cc_final: 0.7337 (ttt) REVERT: E 75 ASP cc_start: 0.8367 (m-30) cc_final: 0.7447 (t70) REVERT: F 148 ASP cc_start: 0.8388 (m-30) cc_final: 0.7921 (m-30) REVERT: G 83 MET cc_start: 0.4835 (mmp) cc_final: 0.4590 (mmm) outliers start: 17 outliers final: 15 residues processed: 140 average time/residue: 0.0724 time to fit residues: 14.9182 Evaluate side-chains 145 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 205 SER Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.185127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.140739 restraints weight = 8837.272| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.01 r_work: 0.3081 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9035 Z= 0.111 Angle : 0.445 8.428 12169 Z= 0.231 Chirality : 0.035 0.131 1447 Planarity : 0.003 0.042 1544 Dihedral : 3.321 13.564 1223 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.70 % Allowed : 26.89 % Favored : 71.41 % 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 are not related in a simple way. whole: 4.16 (0.25), residues: 1149 helix: 3.08 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : -0.26 (0.56), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 216 TYR 0.007 0.001 TYR F 188 PHE 0.013 0.001 PHE A 39 TRP 0.003 0.001 TRP A 18 HIS 0.002 0.001 HIS D 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 9035) covalent geometry : angle 0.44511 / 0.23 (12169) hydrogen bonds : bond 0.03812 / 2.43 ( 812) hydrogen bonds : angle 3.44364 / 2.54 ( 2411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1973.04 seconds wall clock time: 34 minutes 17.73 seconds (2057.73 seconds total)