Starting phenix.real_space_refine on Sat Feb 7 02:37:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d35_46525/02_2026/9d35_46525_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d35_46525/02_2026/9d35_46525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d35_46525/02_2026/9d35_46525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d35_46525/02_2026/9d35_46525.map" model { file = "/net/cci-nas-00/data/ceres_data/9d35_46525/02_2026/9d35_46525_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d35_46525/02_2026/9d35_46525_neut.cif" } resolution = 3.26 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= 0.004 sd= 0.339 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 45 5.16 5 C 9195 2.51 5 N 2464 2.21 5 O 2815 1.98 5 H 14490 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29009 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 3815 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 230} Chain: "B" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 3814 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 236} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3599 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 5, 'TRANS': 226} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3672 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 9, 'TRANS': 223} Chain: "G" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3692 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 9, 'TRANS': 227} Chain: "P" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1281 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "I" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3277 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 4, 'TRANS': 213} Chain breaks: 2 Chain: "J" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2922 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2937 Classifications: {'peptide': 182} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Time building chain proxies: 5.06, per 1000 atoms: 0.17 Number of scatterers: 29009 At special positions: 0 Unit cell: (128.16, 139.908, 124.956, 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 45 16.00 O 2815 8.00 N 2464 7.00 C 9195 6.00 H 14490 1.00 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: 2.55 Conformation dependent library (CDL) restraints added in 907.5 milliseconds 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3444 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 42.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.887A pdb=" N VAL A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 86 through 109 removed outlier: 3.806A pdb=" N GLU A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.643A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.697A pdb=" N LYS A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.672A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 57 through 61 removed outlier: 4.418A pdb=" N LEU B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.717A pdb=" N ILE B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 199 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.614A pdb=" N LEU B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 222' Processing helix chain 'B' and resid 239 through 249 removed outlier: 4.284A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.830A pdb=" N GLU C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.739A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.528A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 200 removed outlier: 3.531A pdb=" N ALA C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 242 removed outlier: 3.709A pdb=" N LYS C 236 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 Processing helix chain 'D' and resid 78 through 100 removed outlier: 3.584A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.560A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.706A pdb=" N CYS D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 removed outlier: 3.670A pdb=" N ILE D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 206 through 210' Processing helix chain 'D' and resid 225 through 246 removed outlier: 5.713A pdb=" N GLN D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 removed outlier: 4.378A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 removed outlier: 3.700A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.873A pdb=" N HIS G 182 " --> pdb=" O LYS G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 204 removed outlier: 4.045A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA G 197 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS G 198 " --> pdb=" O LYS G 194 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 248 Processing helix chain 'I' and resid 9 through 18 Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 118 Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 176 through 192 removed outlier: 3.518A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 removed outlier: 5.001A pdb=" N LEU J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU J 153 " --> pdb=" O MET J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 173 Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.815A pdb=" N GLN K 55 " --> pdb=" O GLY K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 90 Processing helix chain 'K' and resid 136 through 148 removed outlier: 4.127A pdb=" N THR K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE K 141 " --> pdb=" O GLY K 137 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER K 142 " --> pdb=" O PHE K 138 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU K 143 " --> pdb=" O TYR K 139 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS K 146 " --> pdb=" O SER K 142 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'P' and resid 52 through 58 removed outlier: 4.596A pdb=" N THR P 56 " --> pdb=" O PRO P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 Processing helix chain 'P' and resid 79 through 95 removed outlier: 3.596A pdb=" N ASP P 95 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 112 removed outlier: 3.658A pdb=" N ASP P 108 " --> pdb=" O SER P 104 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE P 109 " --> pdb=" O ILE P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 123 525 hydrogen bonds defined for protein. 1575 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: 5.89 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4512 1.04 - 1.24: 11777 1.24 - 1.44: 4447 1.44 - 1.64: 8466 1.64 - 1.84: 72 Bond restraints: 29274 Sorted by residual: bond pdb=" N ARG D 127 " pdb=" H ARG D 127 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" NH1 ARG K 85 " pdb="HH12 ARG K 85 " ideal model delta sigma weight residual 0.860 1.014 -0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" NH2 ARG K 85 " pdb="HH21 ARG K 85 " ideal model delta sigma weight residual 0.860 1.013 -0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" CE2 PHE G 230 " pdb=" HE2 PHE G 230 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N GLN K 166 " pdb=" H GLN K 166 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 29269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 45620 2.76 - 5.53: 5903 5.53 - 8.29: 1367 8.29 - 11.05: 27 11.05 - 13.82: 18 Bond angle restraints: 52935 Sorted by residual: angle pdb=" CA GLY J 52 " pdb=" C GLY J 52 " pdb=" N ILE J 53 " ideal model delta sigma weight residual 115.33 121.29 -5.96 1.15e+00 7.56e-01 2.68e+01 angle pdb=" N THR I 31 " pdb=" CA THR I 31 " pdb=" C THR I 31 " ideal model delta sigma weight residual 110.24 117.27 -7.03 1.41e+00 5.03e-01 2.49e+01 angle pdb=" CA PHE B 157 " pdb=" CB PHE B 157 " pdb=" CG PHE B 157 " ideal model delta sigma weight residual 113.80 118.78 -4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" CA GLY J 140 " pdb=" C GLY J 140 " pdb=" N THR J 141 " ideal model delta sigma weight residual 115.74 119.36 -3.62 7.30e-01 1.88e+00 2.46e+01 angle pdb=" OE1 GLN G 23 " pdb=" CD GLN G 23 " pdb=" NE2 GLN G 23 " ideal model delta sigma weight residual 122.60 117.67 4.93 1.00e+00 1.00e+00 2.43e+01 ... (remaining 52930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 12603 17.96 - 35.92: 793 35.92 - 53.88: 241 53.88 - 71.84: 77 71.84 - 89.80: 22 Dihedral angle restraints: 13736 sinusoidal: 7521 harmonic: 6215 Sorted by residual: dihedral pdb=" CA PRO D 185 " pdb=" C PRO D 185 " pdb=" N ALA D 186 " pdb=" CA ALA D 186 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LEU C 211 " pdb=" C LEU C 211 " pdb=" N GLU C 212 " pdb=" CA GLU C 212 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO A 60 " pdb=" C PRO A 60 " pdb=" N ASP A 61 " pdb=" CA ASP A 61 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 13733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1789 0.122 - 0.244: 438 0.244 - 0.366: 36 0.366 - 0.488: 1 0.488 - 0.610: 3 Chirality restraints: 2267 Sorted by residual: chirality pdb=" CB VAL J 187 " pdb=" CA VAL J 187 " pdb=" CG1 VAL J 187 " pdb=" CG2 VAL J 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" CA VAL J 187 " pdb=" N VAL J 187 " pdb=" C VAL J 187 " pdb=" CB VAL J 187 " both_signs ideal model delta sigma weight residual False 2.44 1.94 0.50 2.00e-01 2.50e+01 6.16e+00 chirality pdb=" CA THR A 129 " pdb=" N THR A 129 " pdb=" C THR A 129 " pdb=" CB THR A 129 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 6.03e+00 ... (remaining 2264 not shown) Planarity restraints: 4353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 96 " -0.058 9.50e-02 1.11e+02 1.97e-01 8.67e+02 pdb=" NE ARG A 96 " -0.168 2.00e-02 2.50e+03 pdb=" CZ ARG A 96 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 96 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 96 " 0.048 2.00e-02 2.50e+03 pdb="HH11 ARG A 96 " 0.399 2.00e-02 2.50e+03 pdb="HH12 ARG A 96 " -0.375 2.00e-02 2.50e+03 pdb="HH21 ARG A 96 " 0.059 2.00e-02 2.50e+03 pdb="HH22 ARG A 96 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 234 " -0.398 9.50e-02 1.11e+02 2.33e-01 8.46e+02 pdb=" NE ARG B 234 " -0.147 2.00e-02 2.50e+03 pdb=" CZ ARG B 234 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG B 234 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 234 " 0.045 2.00e-02 2.50e+03 pdb="HH11 ARG B 234 " 0.391 2.00e-02 2.50e+03 pdb="HH12 ARG B 234 " -0.375 2.00e-02 2.50e+03 pdb="HH21 ARG B 234 " 0.046 2.00e-02 2.50e+03 pdb="HH22 ARG B 234 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 236 " -0.443 9.50e-02 1.11e+02 1.82e-01 2.72e+02 pdb=" NE ARG B 236 " -0.097 2.00e-02 2.50e+03 pdb=" CZ ARG B 236 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 236 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 236 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG B 236 " 0.219 2.00e-02 2.50e+03 pdb="HH12 ARG B 236 " -0.194 2.00e-02 2.50e+03 pdb="HH21 ARG B 236 " 0.060 2.00e-02 2.50e+03 pdb="HH22 ARG B 236 " 0.024 2.00e-02 2.50e+03 ... (remaining 4350 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 740 2.03 - 2.67: 38233 2.67 - 3.32: 87955 3.32 - 3.96: 112895 3.96 - 4.60: 169410 Nonbonded interactions: 409233 Sorted by model distance: nonbonded pdb=" HD1 TRP P 119 " pdb=" HH TYR I 119 " model vdw 1.389 2.100 nonbonded pdb=" OE1 GLU D 189 " pdb=" HH TYR D 232 " model vdw 1.613 2.450 nonbonded pdb=" OE2 GLU B 176 " pdb=" HG1 THR C 55 " model vdw 1.632 2.450 nonbonded pdb=" O GLU G 95 " pdb=" HG SER G 98 " model vdw 1.637 2.450 nonbonded pdb=" OD1 ASP A 89 " pdb="HH22 ARG A 135 " model vdw 1.640 2.450 ... (remaining 409228 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.190 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.500 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.012 0.111 14784 Z= 0.750 Angle : 1.877 9.667 19999 Z= 1.263 Chirality : 0.101 0.610 2267 Planarity : 0.014 0.124 2573 Dihedral : 13.767 89.800 5475 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.52 % Allowed : 5.58 % Favored : 92.90 % Cbeta Deviations : 0.23 % 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: -1.66 (0.17), residues: 1833 helix: -1.23 (0.16), residues: 732 sheet: 0.29 (0.27), residues: 336 loop : -1.50 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 217 TYR 0.112 0.018 TYR I 215 PHE 0.089 0.015 PHE C 135 TRP 0.087 0.018 TRP D 159 HIS 0.011 0.003 HIS K 133 Details of bonding type rmsd covalent geometry : bond 0.01188 (14784) covalent geometry : angle 1.87682 (19999) hydrogen bonds : bond 0.19930 ( 525) hydrogen bonds : angle 7.62657 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 387 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8082 (mtmm) REVERT: A 230 LYS cc_start: 0.9213 (ptmt) cc_final: 0.8979 (tptt) REVERT: A 250 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8124 (tm-30) REVERT: A 251 GLN cc_start: 0.8684 (tt0) cc_final: 0.8356 (tp-100) REVERT: C 181 LYS cc_start: 0.8262 (mmtt) cc_final: 0.8006 (mmtm) REVERT: D 146 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7726 (mmmm) REVERT: D 172 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7495 (ttm110) REVERT: D 216 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8582 (mtmm) REVERT: D 217 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.5999 (Cg_endo) REVERT: D 227 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7940 (tm-30) REVERT: G 68 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8400 (mm-40) REVERT: P 69 MET cc_start: 0.8092 (mmt) cc_final: 0.7830 (mmt) REVERT: P 86 MET cc_start: 0.8674 (mtp) cc_final: 0.8326 (tpp) REVERT: P 89 GLU cc_start: 0.8320 (tp30) cc_final: 0.8005 (tp30) REVERT: I 201 ASN cc_start: 0.7685 (m110) cc_final: 0.7026 (m110) REVERT: I 211 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8837 (mttm) REVERT: J 191 LYS cc_start: 0.9128 (mtpt) cc_final: 0.8867 (mtmm) REVERT: K 45 SER cc_start: 0.8355 (m) cc_final: 0.8138 (p) REVERT: K 143 LEU cc_start: 0.8342 (tp) cc_final: 0.8135 (tp) REVERT: K 155 GLU cc_start: 0.8659 (tt0) cc_final: 0.8401 (tp30) REVERT: K 159 ASP cc_start: 0.8459 (m-30) cc_final: 0.8093 (m-30) REVERT: K 161 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8622 (mt) REVERT: K 176 PHE cc_start: 0.8047 (t80) cc_final: 0.7821 (t80) REVERT: K 177 LYS cc_start: 0.9201 (mmtt) cc_final: 0.8865 (mmtt) REVERT: K 182 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8280 (mtmm) REVERT: K 191 GLN cc_start: 0.8460 (tt0) cc_final: 0.8124 (tm-30) outliers start: 24 outliers final: 11 residues processed: 401 average time/residue: 0.4616 time to fit residues: 238.6492 Evaluate side-chains 282 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain I residue 6 PHE Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain K residue 4 ILE Chi-restraints excluded: chain K residue 161 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS C 227 GLN G 43 ASN P 71 GLN I 95 HIS I 201 ASN ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.062648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.054525 restraints weight = 162952.483| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.82 r_work: 0.3087 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14784 Z= 0.167 Angle : 0.651 6.014 19999 Z= 0.359 Chirality : 0.044 0.150 2267 Planarity : 0.005 0.064 2573 Dihedral : 7.641 71.417 2042 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.97 % Allowed : 10.84 % Favored : 87.19 % 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: -0.62 (0.19), residues: 1833 helix: 0.26 (0.18), residues: 751 sheet: -0.30 (0.25), residues: 378 loop : -1.07 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 86 TYR 0.018 0.002 TYR I 219 PHE 0.019 0.002 PHE J 100 TRP 0.008 0.001 TRP B 159 HIS 0.007 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00360 (14784) covalent geometry : angle 0.65119 (19999) hydrogen bonds : bond 0.05712 ( 525) hydrogen bonds : angle 5.06678 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8791 (mtmm) REVERT: A 210 MET cc_start: 0.7968 (tpt) cc_final: 0.7736 (ttt) REVERT: G 102 LEU cc_start: 0.8534 (mt) cc_final: 0.8320 (mm) REVERT: P 69 MET cc_start: 0.9117 (mmt) cc_final: 0.8734 (mmt) REVERT: P 82 MET cc_start: 0.9205 (tmt) cc_final: 0.8910 (tmt) REVERT: I 173 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8074 (tm-30) REVERT: I 201 ASN cc_start: 0.8271 (m-40) cc_final: 0.8007 (m-40) REVERT: J 15 MET cc_start: 0.8901 (ttm) cc_final: 0.8603 (ttm) REVERT: K 145 ASP cc_start: 0.7314 (t0) cc_final: 0.6892 (t0) outliers start: 31 outliers final: 20 residues processed: 284 average time/residue: 0.4400 time to fit residues: 163.3472 Evaluate side-chains 247 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 204 PHE Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 4 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 11 optimal weight: 0.0010 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 140 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 ASN G 195 GLN ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.062661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.054521 restraints weight = 163524.418| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.84 r_work: 0.3091 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14784 Z= 0.121 Angle : 0.567 6.314 19999 Z= 0.306 Chirality : 0.042 0.143 2267 Planarity : 0.004 0.069 2573 Dihedral : 6.452 65.215 2032 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.59 % Allowed : 13.38 % Favored : 85.03 % 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: -0.08 (0.19), residues: 1833 helix: 0.98 (0.18), residues: 750 sheet: -0.36 (0.24), residues: 391 loop : -0.93 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 67 TYR 0.016 0.001 TYR I 219 PHE 0.018 0.001 PHE K 176 TRP 0.005 0.001 TRP B 159 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00269 (14784) covalent geometry : angle 0.56680 (19999) hydrogen bonds : bond 0.04482 ( 525) hydrogen bonds : angle 4.46800 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8369 (mtt) cc_final: 0.7693 (mtt) REVERT: A 210 MET cc_start: 0.7932 (tpt) cc_final: 0.7731 (ttt) REVERT: D 174 PHE cc_start: 0.8407 (t80) cc_final: 0.8072 (t80) REVERT: G 206 ASP cc_start: 0.9224 (p0) cc_final: 0.8880 (p0) REVERT: P 69 MET cc_start: 0.9078 (mmt) cc_final: 0.8738 (mmt) REVERT: P 82 MET cc_start: 0.9224 (tmt) cc_final: 0.8969 (tmt) REVERT: I 20 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8214 (t-90) REVERT: I 207 MET cc_start: 0.9063 (mtm) cc_final: 0.8814 (mpp) REVERT: K 145 ASP cc_start: 0.7455 (t0) cc_final: 0.7077 (t0) outliers start: 25 outliers final: 14 residues processed: 252 average time/residue: 0.4195 time to fit residues: 139.9147 Evaluate side-chains 235 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 20 TYR Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain I residue 20 HIS Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 193 TRP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 11 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 180 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS D 40 ASN ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.059725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.051645 restraints weight = 164109.290| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.78 r_work: 0.3018 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14784 Z= 0.180 Angle : 0.577 5.794 19999 Z= 0.313 Chirality : 0.043 0.159 2267 Planarity : 0.005 0.066 2573 Dihedral : 6.142 56.519 2026 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.20 % Allowed : 14.97 % Favored : 83.83 % 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: -0.12 (0.19), residues: 1833 helix: 1.10 (0.18), residues: 752 sheet: -0.52 (0.24), residues: 403 loop : -1.06 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 149 TYR 0.018 0.002 TYR I 219 PHE 0.014 0.002 PHE K 138 TRP 0.007 0.001 TRP B 159 HIS 0.007 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00405 (14784) covalent geometry : angle 0.57661 (19999) hydrogen bonds : bond 0.04552 ( 525) hydrogen bonds : angle 4.39926 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8005 (tpt) cc_final: 0.7774 (ttt) REVERT: B 207 ASP cc_start: 0.8093 (t0) cc_final: 0.7889 (t0) REVERT: D 21 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8007 (tm-30) REVERT: D 144 GLU cc_start: 0.7905 (tp30) cc_final: 0.7682 (tp30) REVERT: D 148 TYR cc_start: 0.8852 (m-80) cc_final: 0.8598 (m-80) REVERT: D 188 VAL cc_start: 0.7633 (p) cc_final: 0.7408 (p) REVERT: G 86 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8192 (mmm160) REVERT: P 69 MET cc_start: 0.9092 (mmt) cc_final: 0.8750 (mmt) REVERT: P 82 MET cc_start: 0.9246 (tmt) cc_final: 0.8929 (tmt) REVERT: I 207 MET cc_start: 0.9116 (mtm) cc_final: 0.8847 (mpp) REVERT: J 15 MET cc_start: 0.8901 (ttm) cc_final: 0.8689 (ttm) outliers start: 19 outliers final: 18 residues processed: 246 average time/residue: 0.4193 time to fit residues: 136.5889 Evaluate side-chains 240 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 193 TRP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 149 MET Chi-restraints excluded: chain K residue 161 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 154 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 0.0030 chunk 114 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 ASN ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.058620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050482 restraints weight = 165600.942| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.81 r_work: 0.2979 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14784 Z= 0.211 Angle : 0.595 6.412 19999 Z= 0.322 Chirality : 0.043 0.144 2267 Planarity : 0.005 0.065 2573 Dihedral : 5.937 54.691 2022 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.03 % Allowed : 15.16 % Favored : 82.82 % 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: -0.29 (0.19), residues: 1833 helix: 1.04 (0.18), residues: 750 sheet: -0.58 (0.25), residues: 397 loop : -1.28 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 67 TYR 0.020 0.002 TYR I 219 PHE 0.019 0.002 PHE J 40 TRP 0.007 0.001 TRP B 159 HIS 0.008 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00474 (14784) covalent geometry : angle 0.59467 (19999) hydrogen bonds : bond 0.04695 ( 525) hydrogen bonds : angle 4.45685 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8042 (tpt) cc_final: 0.7830 (ttt) REVERT: D 21 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8011 (tm-30) REVERT: D 148 TYR cc_start: 0.8893 (m-80) cc_final: 0.8555 (m-80) REVERT: D 211 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7993 (tm-30) REVERT: G 76 CYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7377 (p) REVERT: G 134 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8666 (p) REVERT: P 69 MET cc_start: 0.9066 (mmt) cc_final: 0.8736 (mmt) REVERT: P 82 MET cc_start: 0.9229 (tmt) cc_final: 0.8935 (tmt) REVERT: I 173 GLN cc_start: 0.8730 (tp40) cc_final: 0.8528 (tm-30) REVERT: I 207 MET cc_start: 0.9115 (mtm) cc_final: 0.8902 (mpp) REVERT: J 15 MET cc_start: 0.8887 (ttm) cc_final: 0.8674 (ttm) REVERT: K 155 GLU cc_start: 0.8787 (tp30) cc_final: 0.8551 (tp30) outliers start: 32 outliers final: 24 residues processed: 246 average time/residue: 0.4020 time to fit residues: 131.9604 Evaluate side-chains 247 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ASP Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 193 TRP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 112 ASN Chi-restraints excluded: chain K residue 161 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 173 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 ASN ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.058850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050750 restraints weight = 165161.937| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.79 r_work: 0.2988 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14784 Z= 0.169 Angle : 0.570 6.526 19999 Z= 0.307 Chirality : 0.042 0.140 2267 Planarity : 0.004 0.065 2573 Dihedral : 5.695 54.379 2022 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.84 % Allowed : 16.80 % Favored : 81.36 % 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: -0.24 (0.19), residues: 1833 helix: 1.20 (0.18), residues: 754 sheet: -0.68 (0.26), residues: 390 loop : -1.31 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 73 TYR 0.018 0.001 TYR I 219 PHE 0.013 0.001 PHE J 100 TRP 0.006 0.001 TRP C 160 HIS 0.006 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00381 (14784) covalent geometry : angle 0.57021 (19999) hydrogen bonds : bond 0.04367 ( 525) hydrogen bonds : angle 4.32859 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8032 (tpt) cc_final: 0.7819 (ttt) REVERT: D 21 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8000 (tm-30) REVERT: D 148 TYR cc_start: 0.8880 (m-80) cc_final: 0.8538 (m-80) REVERT: D 211 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7988 (tm-30) REVERT: G 134 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8677 (p) REVERT: P 67 ARG cc_start: 0.9210 (ttm-80) cc_final: 0.8952 (ttm110) REVERT: P 69 MET cc_start: 0.9080 (mmt) cc_final: 0.8772 (mmt) REVERT: P 82 MET cc_start: 0.9222 (tmt) cc_final: 0.8896 (tmt) REVERT: I 173 GLN cc_start: 0.8701 (tp40) cc_final: 0.8492 (tm-30) REVERT: J 15 MET cc_start: 0.8884 (ttm) cc_final: 0.8673 (ttm) REVERT: K 11 ASP cc_start: 0.9128 (p0) cc_final: 0.8820 (p0) REVERT: K 155 GLU cc_start: 0.8827 (tp30) cc_final: 0.8595 (tp30) outliers start: 29 outliers final: 23 residues processed: 252 average time/residue: 0.3673 time to fit residues: 124.0453 Evaluate side-chains 246 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 193 TRP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 112 ASN Chi-restraints excluded: chain K residue 161 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 119 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 ASN ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.059455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051261 restraints weight = 165023.645| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.85 r_work: 0.3003 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14784 Z= 0.134 Angle : 0.547 7.083 19999 Z= 0.293 Chirality : 0.042 0.139 2267 Planarity : 0.004 0.064 2573 Dihedral : 5.443 53.268 2022 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.65 % Allowed : 17.56 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.20), residues: 1833 helix: 1.44 (0.18), residues: 753 sheet: -0.67 (0.26), residues: 397 loop : -1.26 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 141 TYR 0.019 0.001 TYR I 219 PHE 0.012 0.001 PHE I 37 TRP 0.006 0.001 TRP B 179 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00303 (14784) covalent geometry : angle 0.54703 (19999) hydrogen bonds : bond 0.04035 ( 525) hydrogen bonds : angle 4.18855 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.7988 (tpt) cc_final: 0.7787 (ttt) REVERT: B 107 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8894 (t) REVERT: B 207 ASP cc_start: 0.7929 (t0) cc_final: 0.7665 (t0) REVERT: G 134 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8671 (p) REVERT: P 69 MET cc_start: 0.9069 (mmt) cc_final: 0.8776 (mmt) REVERT: P 82 MET cc_start: 0.9223 (tmt) cc_final: 0.8915 (tmt) REVERT: I 173 GLN cc_start: 0.8634 (tp40) cc_final: 0.8422 (tm-30) REVERT: K 11 ASP cc_start: 0.9139 (p0) cc_final: 0.8852 (p0) outliers start: 26 outliers final: 18 residues processed: 245 average time/residue: 0.3722 time to fit residues: 122.1131 Evaluate side-chains 244 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 193 TRP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 112 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 9 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 133 HIS ** 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 = 0.3272 r_free = 0.3272 target = 0.058216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050049 restraints weight = 165675.254| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.84 r_work: 0.2967 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14784 Z= 0.200 Angle : 0.587 6.626 19999 Z= 0.317 Chirality : 0.043 0.150 2267 Planarity : 0.005 0.084 2573 Dihedral : 5.574 52.442 2022 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.78 % Allowed : 17.88 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 1833 helix: 1.32 (0.18), residues: 751 sheet: -0.87 (0.25), residues: 404 loop : -1.36 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 141 TYR 0.019 0.002 TYR I 219 PHE 0.015 0.002 PHE C 131 TRP 0.012 0.001 TRP B 179 HIS 0.008 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00451 (14784) covalent geometry : angle 0.58748 (19999) hydrogen bonds : bond 0.04429 ( 525) hydrogen bonds : angle 4.32653 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 ASP cc_start: 0.8041 (t0) cc_final: 0.7739 (t0) REVERT: G 134 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8757 (p) REVERT: P 69 MET cc_start: 0.9052 (mmt) cc_final: 0.8763 (mmt) REVERT: I 173 GLN cc_start: 0.8735 (tp40) cc_final: 0.8531 (tm-30) REVERT: K 55 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8652 (tm-30) outliers start: 28 outliers final: 22 residues processed: 241 average time/residue: 0.4090 time to fit residues: 131.3625 Evaluate side-chains 244 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 193 TRP Chi-restraints excluded: chain I residue 201 ASN Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 112 ASN Chi-restraints excluded: chain K residue 161 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.0370 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 40 ASN ** K 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051083 restraints weight = 165083.967| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.86 r_work: 0.2993 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14784 Z= 0.131 Angle : 0.560 9.237 19999 Z= 0.299 Chirality : 0.042 0.139 2267 Planarity : 0.005 0.063 2573 Dihedral : 5.259 51.895 2020 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.46 % Allowed : 18.45 % Favored : 80.09 % 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: -0.08 (0.20), residues: 1833 helix: 1.55 (0.18), residues: 752 sheet: -0.88 (0.26), residues: 397 loop : -1.31 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 141 TYR 0.019 0.001 TYR I 219 PHE 0.015 0.001 PHE C 131 TRP 0.011 0.001 TRP B 179 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00297 (14784) covalent geometry : angle 0.55969 (19999) hydrogen bonds : bond 0.03973 ( 525) hydrogen bonds : angle 4.16918 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 ASP cc_start: 0.7991 (t0) cc_final: 0.7680 (t0) REVERT: G 134 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8728 (p) REVERT: P 67 ARG cc_start: 0.9264 (ttm-80) cc_final: 0.9026 (ttm110) REVERT: P 69 MET cc_start: 0.9036 (mmt) cc_final: 0.8763 (mmt) REVERT: K 11 ASP cc_start: 0.9156 (p0) cc_final: 0.8816 (p0) REVERT: K 55 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8658 (tm-30) REVERT: K 172 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8391 (tpt) outliers start: 23 outliers final: 19 residues processed: 241 average time/residue: 0.4086 time to fit residues: 130.9607 Evaluate side-chains 244 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 193 TRP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 112 ASN Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 172 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 154 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 119 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 133 HIS ** 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 = 0.3326 r_free = 0.3326 target = 0.059860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051797 restraints weight = 163042.290| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.80 r_work: 0.3026 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14784 Z= 0.112 Angle : 0.546 7.052 19999 Z= 0.290 Chirality : 0.041 0.139 2267 Planarity : 0.004 0.064 2573 Dihedral : 4.995 51.135 2020 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.33 % Allowed : 18.58 % Favored : 80.09 % 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: 0.17 (0.20), residues: 1833 helix: 1.83 (0.19), residues: 755 sheet: -0.86 (0.26), residues: 392 loop : -1.22 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 120 TYR 0.019 0.001 TYR I 219 PHE 0.015 0.001 PHE C 131 TRP 0.009 0.001 TRP B 179 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00257 (14784) covalent geometry : angle 0.54627 (19999) hydrogen bonds : bond 0.03660 ( 525) hydrogen bonds : angle 4.00177 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3666 Ramachandran restraints generated. 1833 Oldfield, 0 Emsley, 1833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 ASP cc_start: 0.7894 (t0) cc_final: 0.7592 (t0) REVERT: G 134 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8735 (p) REVERT: P 67 ARG cc_start: 0.9237 (ttm-80) cc_final: 0.9008 (ttm110) REVERT: P 69 MET cc_start: 0.8998 (mmt) cc_final: 0.8739 (mmt) REVERT: K 11 ASP cc_start: 0.9152 (p0) cc_final: 0.8812 (p0) REVERT: K 55 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8651 (tm-30) outliers start: 21 outliers final: 18 residues processed: 242 average time/residue: 0.4045 time to fit residues: 130.3707 Evaluate side-chains 245 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain C residue 103 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain G residue 57 LYS Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain P residue 100 SER Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 193 TRP Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 45 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 133 HIS ** 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 = 0.3276 r_free = 0.3276 target = 0.058056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.050012 restraints weight = 164870.368| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.80 r_work: 0.2956 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14784 Z= 0.192 Angle : 0.595 10.494 19999 Z= 0.317 Chirality : 0.042 0.144 2267 Planarity : 0.005 0.064 2573 Dihedral : 5.210 50.512 2020 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.27 % Allowed : 18.90 % Favored : 79.84 % 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: -0.10 (0.20), residues: 1833 helix: 1.62 (0.18), residues: 754 sheet: -0.88 (0.26), residues: 387 loop : -1.47 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 141 TYR 0.017 0.002 TYR C 122 PHE 0.012 0.002 PHE J 100 TRP 0.013 0.001 TRP B 179 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00436 (14784) covalent geometry : angle 0.59502 (19999) hydrogen bonds : bond 0.04219 ( 525) hydrogen bonds : angle 4.19382 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7722.20 seconds wall clock time: 131 minutes 44.72 seconds (7904.72 seconds total)