Starting phenix.real_space_refine on Thu Jul 2 12:39:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyv_60580/07_2026/8zyv_60580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyv_60580/07_2026/8zyv_60580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zyv_60580/07_2026/8zyv_60580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyv_60580/07_2026/8zyv_60580.map" model { file = "/net/cci-nas-00/data/ceres_data/8zyv_60580/07_2026/8zyv_60580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyv_60580/07_2026/8zyv_60580.cif" } resolution = 3.12 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= 0.015 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 77 5.16 5 Na 2 4.78 5 C 5741 2.51 5 N 1469 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 8913 Number of models: 1 Model: "" Number of chains: 10 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: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1601 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 1 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: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 2 Ad-hoc single atom residues: {' NA': 2} Classifications: {'water': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="NA NA A 502 " occ=0.97 residue: pdb=" O HOH A 601 " occ=0.65 residue: pdb=" O HOH E 602 " occ=0.97 residue: pdb=" O HOH G 301 " occ=0.42 Time building chain proxies: 1.92, per 1000 atoms: 0.22 Number of scatterers: 8913 At special positions: 0 Unit cell: (102.6, 98.55, 105.3, 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 77 16.00 Na 2 11.00 O 1624 8.00 N 1469 7.00 C 5741 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: 0.53 Conformation dependent library (CDL) restraints added in 431.0 milliseconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 1 sheets defined 91.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.877A pdb=" N GLY A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.884A 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: 3.956A 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 Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.974A pdb=" N ASP C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 167 removed outlier: 3.639A 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: 3.939A pdb=" N MET C 179 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA C 180 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 181 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 3.952A 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 'D' and resid 31 through 47 Processing helix chain 'D' and resid 51 through 68 Processing helix chain 'D' and resid 72 through 87 removed outlier: 3.964A pdb=" N ASP D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA D 86 " --> pdb=" O GLU D 82 " (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: 3.734A pdb=" N VAL D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.900A 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: 4.293A pdb=" N ILE D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP D 235 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.556A pdb=" N ARG D 247 " --> pdb=" O GLU D 244 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 249 " --> pdb=" O LYS D 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 48 removed outlier: 3.565A pdb=" N ASP E 31 " --> pdb=" O GLY E 27 " (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: 3.807A 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 248 removed outlier: 6.723A pdb=" N GLY E 245 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS E 246 " --> pdb=" O ASN E 243 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 248 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 23 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.564A 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 removed outlier: 3.866A pdb=" N GLY F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 168 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 196 removed outlier: 3.686A pdb=" N THR F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET F 195 " --> pdb=" O ILE F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 228 Processing helix chain 'F' and resid 230 through 243 Processing helix chain 'F' and resid 244 through 251 removed outlier: 3.546A pdb=" N ARG F 247 " --> pdb=" O GLU F 244 " (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 113 Processing helix chain 'G' and resid 117 through 169 removed outlier: 4.142A pdb=" N VAL G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 171 through 196 removed outlier: 3.564A 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 238 Processing helix chain 'G' and resid 238 through 243 removed outlier: 3.611A pdb=" N ASN G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 244 through 250 removed outlier: 3.659A 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 42 815 hydrogen bonds defined for protein. 2412 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: 1.37 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2896 1.35 - 1.46: 1873 1.46 - 1.58: 4108 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 9029 Sorted by residual: bond pdb=" CB MET C 179 " pdb=" CG MET C 179 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.47e+00 bond pdb=" CG MET C 179 " pdb=" SD MET C 179 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.46e+00 bond pdb=" CB ASP G 75 " pdb=" CG ASP G 75 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.93e-01 bond pdb=" CB ILE D 61 " pdb=" CG1 ILE D 61 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.64e-01 bond pdb=" CA PRO D 172 " pdb=" CB PRO D 172 " ideal model delta sigma weight residual 1.532 1.537 -0.006 7.10e-03 1.98e+04 6.59e-01 ... (remaining 9024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 11943 1.47 - 2.94: 158 2.94 - 4.41: 45 4.41 - 5.88: 12 5.88 - 7.35: 2 Bond angle restraints: 12160 Sorted by residual: angle pdb=" CG MET C 179 " pdb=" SD MET C 179 " pdb=" CE MET C 179 " ideal model delta sigma weight residual 100.90 94.42 6.48 2.20e+00 2.07e-01 8.68e+00 angle pdb=" N MET F 67 " pdb=" CA MET F 67 " pdb=" C MET F 67 " ideal model delta sigma weight residual 111.03 113.90 -2.87 1.11e+00 8.12e-01 6.70e+00 angle pdb=" N GLY E 245 " pdb=" CA GLY E 245 " pdb=" C GLY E 245 " ideal model delta sigma weight residual 110.86 115.21 -4.35 1.84e+00 2.95e-01 5.58e+00 angle pdb=" CA MET D 105 " pdb=" CB MET D 105 " pdb=" CG MET D 105 " ideal model delta sigma weight residual 114.10 118.38 -4.28 2.00e+00 2.50e-01 4.58e+00 angle pdb=" CA LEU D 213 " pdb=" CB LEU D 213 " pdb=" CG LEU D 213 " ideal model delta sigma weight residual 116.30 123.65 -7.35 3.50e+00 8.16e-02 4.41e+00 ... (remaining 12155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4572 17.50 - 35.00: 636 35.00 - 52.50: 194 52.50 - 70.00: 31 70.00 - 87.50: 10 Dihedral angle restraints: 5443 sinusoidal: 2129 harmonic: 3314 Sorted by residual: dihedral pdb=" CA ASP F 220 " pdb=" CB ASP F 220 " pdb=" CG ASP F 220 " pdb=" OD1 ASP F 220 " ideal model delta sinusoidal sigma weight residual -30.00 -87.57 57.57 1 2.00e+01 2.50e-03 1.11e+01 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 -87.01 57.01 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASP E 85 " pdb=" CB ASP E 85 " pdb=" CG ASP E 85 " pdb=" OD1 ASP E 85 " ideal model delta sinusoidal sigma weight residual -30.00 -85.26 55.26 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 5440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 931 0.027 - 0.054: 317 0.054 - 0.081: 150 0.081 - 0.108: 39 0.108 - 0.135: 9 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA ASP C 148 " pdb=" N ASP C 148 " pdb=" C ASP C 148 " pdb=" CB ASP C 148 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.57e-01 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 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CG LEU D 166 " pdb=" CB LEU D 166 " pdb=" CD1 LEU D 166 " pdb=" CD2 LEU D 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 1443 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 180 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C ALA C 180 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA C 180 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C 181 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 15 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO B 16 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 37 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C ILE G 37 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE G 37 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL G 38 " 0.010 2.00e-02 2.50e+03 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 210 2.72 - 3.26: 9197 3.26 - 3.81: 15322 3.81 - 4.35: 17308 4.35 - 4.90: 30752 Nonbonded interactions: 72789 Sorted by model distance: nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 188 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR E 158 " pdb=" OG1 THR E 186 " model vdw 2.202 3.040 nonbonded pdb=" O LEU A 35 " pdb=" OG SER A 38 " model vdw 2.231 3.040 nonbonded pdb=" OD1 ASP E 31 " pdb=" OH TYR E 188 " model vdw 2.293 3.040 nonbonded pdb=" O VAL F 38 " pdb=" OG SER F 42 " model vdw 2.318 3.040 ... (remaining 72784 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' and resid 14 through 59) selection = (chain 'B' and resid 14 through 59) } ncs_group { reference = (chain 'C' and resid 29 through 250) selection = (chain 'D' and resid 29 through 250) selection = (chain 'E' and resid 29 through 250) selection = (chain 'F' and (resid 15 through 16 or resid 31 through 250)) selection = (chain 'G' and resid 29 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=0.42 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.130 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9029 Z= 0.121 Angle : 0.488 7.347 12160 Z= 0.259 Chirality : 0.035 0.135 1446 Planarity : 0.004 0.045 1543 Dihedral : 17.749 87.504 3305 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.43 % Allowed : 27.98 % Favored : 71.60 % 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: 3.33 (0.25), residues: 1148 helix: 2.57 (0.16), residues: 998 sheet: None (None), residues: 0 loop : -0.47 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 215 TYR 0.014 0.001 TYR F 241 PHE 0.019 0.001 PHE A 32 TRP 0.007 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 9029) covalent geometry : angle 0.48802 / 0.26 (12160) hydrogen bonds : bond 0.12792 / 8.32 ( 815) hydrogen bonds : angle 5.07470 / 3.64 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.303 Fit side-chains REVERT: C 149 VAL cc_start: 0.8627 (p) cc_final: 0.8422 (t) REVERT: D 75 ASP cc_start: 0.7664 (m-30) cc_final: 0.7139 (t70) REVERT: F 67 MET cc_start: 0.8345 (mtm) cc_final: 0.8119 (mtm) REVERT: G 75 ASP cc_start: 0.7105 (t0) cc_final: 0.6798 (t0) outliers start: 4 outliers final: 2 residues processed: 154 average time/residue: 0.0715 time to fit residues: 15.2581 Evaluate side-chains 152 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain F residue 51 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.182169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118474 restraints weight = 8886.856| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.82 r_work: 0.2985 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9029 Z= 0.128 Angle : 0.455 5.299 12160 Z= 0.240 Chirality : 0.036 0.119 1446 Planarity : 0.004 0.044 1543 Dihedral : 3.656 40.368 1224 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.60 % Allowed : 25.96 % Favored : 72.45 % 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: 3.78 (0.25), residues: 1148 helix: 2.89 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -0.50 (0.51), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 215 TYR 0.009 0.001 TYR F 241 PHE 0.023 0.001 PHE A 32 TRP 0.005 0.002 TRP A 18 HIS 0.003 0.001 HIS G 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9029) covalent geometry : angle 0.45526 / 0.24 (12160) hydrogen bonds : bond 0.04146 / 2.66 ( 815) hydrogen bonds : angle 3.80618 / 2.78 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.204 Fit side-chains REVERT: D 64 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7590 (ttmt) REVERT: F 67 MET cc_start: 0.8421 (mtm) cc_final: 0.8177 (mtm) REVERT: F 83 MET cc_start: 0.7564 (mtt) cc_final: 0.7097 (mtp) REVERT: G 75 ASP cc_start: 0.7341 (t0) cc_final: 0.6836 (t0) outliers start: 15 outliers final: 7 residues processed: 161 average time/residue: 0.0809 time to fit residues: 17.8890 Evaluate side-chains 159 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 0.0070 chunk 29 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.181301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.115999 restraints weight = 8826.490| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.63 r_work: 0.2999 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9029 Z= 0.117 Angle : 0.433 6.433 12160 Z= 0.228 Chirality : 0.035 0.116 1446 Planarity : 0.004 0.045 1543 Dihedral : 3.303 13.197 1221 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.38 % Allowed : 25.64 % Favored : 72.98 % 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: 3.96 (0.25), residues: 1148 helix: 3.03 (0.16), residues: 998 sheet: None (None), residues: 0 loop : -0.54 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 215 TYR 0.007 0.001 TYR F 241 PHE 0.026 0.001 PHE A 32 TRP 0.005 0.001 TRP A 18 HIS 0.003 0.001 HIS G 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9029) covalent geometry : angle 0.43333 / 0.23 (12160) hydrogen bonds : bond 0.03902 / 2.50 ( 815) hydrogen bonds : angle 3.67210 / 2.69 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.299 Fit side-chains REVERT: D 128 ASP cc_start: 0.6423 (t0) cc_final: 0.6221 (t0) REVERT: F 83 MET cc_start: 0.7516 (mtt) cc_final: 0.7161 (mtp) REVERT: G 75 ASP cc_start: 0.7507 (t0) cc_final: 0.7070 (t0) outliers start: 13 outliers final: 9 residues processed: 164 average time/residue: 0.0720 time to fit residues: 16.5561 Evaluate side-chains 160 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 61 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.182087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116761 restraints weight = 8987.478| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.66 r_work: 0.3012 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9029 Z= 0.110 Angle : 0.426 6.629 12160 Z= 0.223 Chirality : 0.035 0.113 1446 Planarity : 0.004 0.044 1543 Dihedral : 3.245 12.894 1221 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.02 % Allowed : 25.32 % Favored : 72.66 % 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: 4.08 (0.25), residues: 1148 helix: 3.09 (0.16), residues: 1006 sheet: None (None), residues: 0 loop : -0.58 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 215 TYR 0.006 0.001 TYR F 241 PHE 0.029 0.001 PHE A 32 TRP 0.005 0.001 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 9029) covalent geometry : angle 0.42572 / 0.22 (12160) hydrogen bonds : bond 0.03722 / 2.38 ( 815) hydrogen bonds : angle 3.59954 / 2.64 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.186 Fit side-chains REVERT: D 112 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.4961 (mm) REVERT: F 83 MET cc_start: 0.7454 (mtt) cc_final: 0.7086 (mtp) REVERT: F 165 MET cc_start: 0.9206 (ttp) cc_final: 0.8887 (tmm) REVERT: G 75 ASP cc_start: 0.7457 (t0) cc_final: 0.7079 (t0) outliers start: 19 outliers final: 13 residues processed: 158 average time/residue: 0.0796 time to fit residues: 17.3078 Evaluate side-chains 162 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.178314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114147 restraints weight = 8878.051| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.71 r_work: 0.2933 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9029 Z= 0.167 Angle : 0.482 7.840 12160 Z= 0.251 Chirality : 0.037 0.129 1446 Planarity : 0.004 0.046 1543 Dihedral : 3.424 13.803 1221 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.77 % Allowed : 25.32 % Favored : 71.91 % 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: 3.68 (0.25), residues: 1148 helix: 2.81 (0.16), residues: 1007 sheet: None (None), residues: 0 loop : -0.58 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 207 TYR 0.009 0.001 TYR F 241 PHE 0.016 0.002 PHE D 143 TRP 0.005 0.002 TRP B 18 HIS 0.005 0.001 HIS G 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 9029) covalent geometry : angle 0.48212 / 0.25 (12160) hydrogen bonds : bond 0.04268 / 2.74 ( 815) hydrogen bonds : angle 3.76394 / 2.76 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.298 Fit side-chains REVERT: A 32 PHE cc_start: 0.7760 (t80) cc_final: 0.7545 (t80) REVERT: C 179 MET cc_start: 0.8043 (mmm) cc_final: 0.7668 (mmm) REVERT: D 100 ILE cc_start: 0.5862 (OUTLIER) cc_final: 0.5475 (pt) REVERT: D 112 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.5117 (mm) REVERT: F 67 MET cc_start: 0.8549 (mtm) cc_final: 0.8273 (mtp) REVERT: F 83 MET cc_start: 0.7454 (mtt) cc_final: 0.7136 (mtm) REVERT: F 134 GLU cc_start: 0.8359 (tp30) cc_final: 0.7992 (mm-30) REVERT: F 165 MET cc_start: 0.9243 (ttp) cc_final: 0.8908 (tmm) REVERT: F 169 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8676 (ttt) REVERT: F 239 LYS cc_start: 0.7254 (mmtm) cc_final: 0.7029 (mmtm) REVERT: G 75 ASP cc_start: 0.7535 (t0) cc_final: 0.7285 (t0) outliers start: 26 outliers final: 18 residues processed: 170 average time/residue: 0.0797 time to fit residues: 18.9167 Evaluate side-chains 178 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.177123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.115516 restraints weight = 8940.642| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.73 r_work: 0.2914 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9029 Z= 0.181 Angle : 0.499 6.669 12160 Z= 0.261 Chirality : 0.038 0.133 1446 Planarity : 0.004 0.046 1543 Dihedral : 3.532 14.080 1221 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.09 % Allowed : 25.43 % Favored : 71.49 % 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: 3.43 (0.25), residues: 1148 helix: 2.64 (0.16), residues: 1007 sheet: None (None), residues: 0 loop : -0.71 (0.47), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 207 TYR 0.008 0.001 TYR F 241 PHE 0.017 0.002 PHE D 143 TRP 0.007 0.002 TRP B 18 HIS 0.006 0.001 HIS G 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 9029) covalent geometry : angle 0.49865 / 0.26 (12160) hydrogen bonds : bond 0.04455 / 2.86 ( 815) hydrogen bonds : angle 3.83941 / 2.82 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.230 Fit side-chains REVERT: C 179 MET cc_start: 0.8027 (mmm) cc_final: 0.7691 (mmm) REVERT: D 100 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5459 (pt) REVERT: D 112 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.4964 (mm) REVERT: F 67 MET cc_start: 0.8528 (mtm) cc_final: 0.8266 (mtp) REVERT: F 83 MET cc_start: 0.7477 (mtt) cc_final: 0.7226 (mtp) REVERT: F 134 GLU cc_start: 0.8362 (tp30) cc_final: 0.7982 (mm-30) REVERT: F 169 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8727 (ttt) REVERT: G 75 ASP cc_start: 0.7585 (t0) cc_final: 0.7356 (t0) outliers start: 29 outliers final: 22 residues processed: 176 average time/residue: 0.0739 time to fit residues: 18.3028 Evaluate side-chains 182 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 169 MET Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 175 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.181699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.114216 restraints weight = 8910.813| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.71 r_work: 0.2974 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9029 Z= 0.114 Angle : 0.432 6.658 12160 Z= 0.228 Chirality : 0.035 0.134 1446 Planarity : 0.004 0.046 1543 Dihedral : 3.342 13.155 1221 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.23 % Allowed : 26.91 % Favored : 70.85 % 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: 3.88 (0.25), residues: 1148 helix: 2.95 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -0.69 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 215 TYR 0.005 0.001 TYR F 241 PHE 0.012 0.001 PHE A 39 TRP 0.006 0.002 TRP A 18 HIS 0.002 0.000 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9029) covalent geometry : angle 0.43189 / 0.23 (12160) hydrogen bonds : bond 0.03752 / 2.40 ( 815) hydrogen bonds : angle 3.65327 / 2.68 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.228 Fit side-chains REVERT: C 179 MET cc_start: 0.7865 (mmm) cc_final: 0.7535 (mmm) REVERT: D 100 ILE cc_start: 0.5732 (OUTLIER) cc_final: 0.5238 (pt) REVERT: D 112 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5049 (mm) REVERT: F 67 MET cc_start: 0.8498 (mtm) cc_final: 0.8259 (mtp) REVERT: F 83 MET cc_start: 0.7516 (mtt) cc_final: 0.7200 (mtm) REVERT: G 75 ASP cc_start: 0.7615 (t0) cc_final: 0.7276 (t0) outliers start: 21 outliers final: 16 residues processed: 164 average time/residue: 0.0769 time to fit residues: 17.4703 Evaluate side-chains 169 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.182070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.114880 restraints weight = 8848.287| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.72 r_work: 0.2993 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9029 Z= 0.111 Angle : 0.438 6.937 12160 Z= 0.230 Chirality : 0.035 0.137 1446 Planarity : 0.004 0.046 1543 Dihedral : 3.277 13.215 1221 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.23 % Allowed : 27.45 % Favored : 70.32 % 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: 4.01 (0.24), residues: 1148 helix: 3.04 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -0.49 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 215 TYR 0.005 0.001 TYR F 241 PHE 0.013 0.001 PHE A 32 TRP 0.006 0.001 TRP A 18 HIS 0.003 0.001 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9029) covalent geometry : angle 0.43751 / 0.23 (12160) hydrogen bonds : bond 0.03688 / 2.36 ( 815) hydrogen bonds : angle 3.64023 / 2.66 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.234 Fit side-chains REVERT: C 179 MET cc_start: 0.7863 (mmm) cc_final: 0.7635 (mmm) REVERT: D 100 ILE cc_start: 0.5789 (OUTLIER) cc_final: 0.5301 (pt) REVERT: D 112 LEU cc_start: 0.5394 (OUTLIER) cc_final: 0.5054 (mm) REVERT: D 165 MET cc_start: 0.8648 (ttt) cc_final: 0.8295 (tmm) REVERT: F 67 MET cc_start: 0.8444 (mtm) cc_final: 0.8188 (mtp) REVERT: F 83 MET cc_start: 0.7453 (mtt) cc_final: 0.7087 (mtp) REVERT: G 75 ASP cc_start: 0.7634 (t0) cc_final: 0.7318 (t0) outliers start: 21 outliers final: 15 residues processed: 165 average time/residue: 0.0742 time to fit residues: 16.9701 Evaluate side-chains 166 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.179162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.112492 restraints weight = 8874.335| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.68 r_work: 0.2955 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9029 Z= 0.145 Angle : 0.479 7.066 12160 Z= 0.248 Chirality : 0.037 0.134 1446 Planarity : 0.004 0.046 1543 Dihedral : 3.388 13.616 1221 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.02 % Allowed : 27.66 % Favored : 70.32 % 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: 3.79 (0.24), residues: 1148 helix: 2.89 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -0.48 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 207 TYR 0.008 0.001 TYR F 241 PHE 0.014 0.001 PHE D 143 TRP 0.005 0.002 TRP B 18 HIS 0.004 0.001 HIS G 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 9029) covalent geometry : angle 0.47905 / 0.25 (12160) hydrogen bonds : bond 0.04045 / 2.60 ( 815) hydrogen bonds : angle 3.74481 / 2.74 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.179 Fit side-chains REVERT: C 179 MET cc_start: 0.7872 (mmm) cc_final: 0.7310 (mmm) REVERT: D 100 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5196 (pt) REVERT: D 112 LEU cc_start: 0.5376 (OUTLIER) cc_final: 0.5074 (mm) REVERT: D 165 MET cc_start: 0.8625 (ttt) cc_final: 0.8384 (tmm) REVERT: F 67 MET cc_start: 0.8471 (mtm) cc_final: 0.8241 (mtp) REVERT: F 83 MET cc_start: 0.7523 (mtt) cc_final: 0.7181 (mtm) REVERT: G 75 ASP cc_start: 0.7684 (t0) cc_final: 0.7370 (t0) outliers start: 19 outliers final: 16 residues processed: 163 average time/residue: 0.0753 time to fit residues: 17.1350 Evaluate side-chains 168 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.182193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118824 restraints weight = 8887.578| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.79 r_work: 0.2971 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9029 Z= 0.114 Angle : 0.449 7.160 12160 Z= 0.233 Chirality : 0.035 0.132 1446 Planarity : 0.004 0.046 1543 Dihedral : 3.296 13.111 1221 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.91 % Allowed : 27.77 % Favored : 70.32 % 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: 1148 helix: 3.04 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -0.49 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 215 TYR 0.006 0.001 TYR F 241 PHE 0.011 0.001 PHE A 39 TRP 0.006 0.001 TRP A 18 HIS 0.002 0.001 HIS G 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9029) covalent geometry : angle 0.44862 / 0.23 (12160) hydrogen bonds : bond 0.03699 / 2.36 ( 815) hydrogen bonds : angle 3.65288 / 2.67 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.333 Fit side-chains REVERT: C 179 MET cc_start: 0.8043 (mmm) cc_final: 0.7486 (mmm) REVERT: D 100 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5169 (pt) REVERT: D 112 LEU cc_start: 0.5404 (OUTLIER) cc_final: 0.5084 (mm) REVERT: D 165 MET cc_start: 0.8608 (ttt) cc_final: 0.8252 (tmm) REVERT: F 67 MET cc_start: 0.8455 (mtm) cc_final: 0.8233 (mtp) REVERT: F 83 MET cc_start: 0.7536 (mtt) cc_final: 0.7158 (mtp) REVERT: G 75 ASP cc_start: 0.7703 (t0) cc_final: 0.7413 (t0) outliers start: 18 outliers final: 16 residues processed: 157 average time/residue: 0.0784 time to fit residues: 17.2827 Evaluate side-chains 164 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain G residue 155 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 9 optimal weight: 0.0570 chunk 74 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.183432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117003 restraints weight = 8745.195| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.81 r_work: 0.3007 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9029 Z= 0.107 Angle : 0.441 7.192 12160 Z= 0.229 Chirality : 0.035 0.132 1446 Planarity : 0.004 0.046 1543 Dihedral : 3.221 12.511 1221 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.91 % Allowed : 27.87 % Favored : 70.21 % 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: 4.12 (0.24), residues: 1148 helix: 3.12 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -0.45 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 215 TYR 0.006 0.001 TYR F 241 PHE 0.012 0.001 PHE A 39 TRP 0.006 0.001 TRP A 18 HIS 0.002 0.001 HIS E 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 9029) covalent geometry : angle 0.44106 / 0.23 (12160) hydrogen bonds : bond 0.03563 / 2.27 ( 815) hydrogen bonds : angle 3.58997 / 2.62 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.33 seconds wall clock time: 36 minutes 52.00 seconds (2212.00 seconds total)