Starting phenix.real_space_refine on Sat Aug 23 00:24:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cea_16602/08_2025/8cea_16602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cea_16602/08_2025/8cea_16602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cea_16602/08_2025/8cea_16602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cea_16602/08_2025/8cea_16602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cea_16602/08_2025/8cea_16602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cea_16602/08_2025/8cea_16602.map" } resolution = 3.94 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= 0.003 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 5858 2.51 5 N 1550 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8970 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "C" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "D" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 538 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "a" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Time building chain proxies: 1.88, per 1000 atoms: 0.21 Number of scatterers: 8970 At special positions: 0 Unit cell: (107.42, 83.64, 112.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1519 8.00 N 1550 7.00 C 5858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 218.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 68.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 70 through 76 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.242A pdb=" N TYR A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.532A pdb=" N GLN A 128 " --> pdb=" O PRO A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 removed outlier: 3.766A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 removed outlier: 3.713A pdb=" N THR A 145 " --> pdb=" O LEU A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.651A pdb=" N VAL A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.233A pdb=" N HIS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 4.171A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 66 removed outlier: 3.959A pdb=" N LEU B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ARG B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 3.695A pdb=" N TRP B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 71 through 76 removed outlier: 4.423A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 88 through 105 removed outlier: 3.590A pdb=" N VAL B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 4.094A pdb=" N LEU B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Proline residue: B 113 - end of helix removed outlier: 3.735A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 151 Proline residue: B 138 - end of helix Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 158 through 185 removed outlier: 4.115A pdb=" N SER B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Proline residue: B 167 - end of helix Proline residue: B 171 - end of helix removed outlier: 3.639A pdb=" N MET B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 220 Proline residue: B 208 - end of helix removed outlier: 3.600A pdb=" N ALA B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 42 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 51 through 54 Processing helix chain 'C' and resid 55 through 84 removed outlier: 4.159A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 3.973A pdb=" N ILE C 80 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 115 removed outlier: 4.180A pdb=" N LEU C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix removed outlier: 3.567A pdb=" N GLY C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 128 through 147 Processing helix chain 'C' and resid 152 through 177 Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 199 through 229 removed outlier: 3.657A pdb=" N GLU C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 243 removed outlier: 3.837A pdb=" N SER C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 69 removed outlier: 3.574A pdb=" N VAL D 21 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Proline residue: D 31 - end of helix Processing helix chain 'a' and resid 41 through 51 removed outlier: 3.545A pdb=" N THR a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 75 Processing helix chain 'a' and resid 92 through 100 removed outlier: 4.310A pdb=" N TYR a 100 " --> pdb=" O ASN a 96 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 117 removed outlier: 3.679A pdb=" N ALA a 116 " --> pdb=" O ALA a 112 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY a 117 " --> pdb=" O LEU a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 129 Processing helix chain 'a' and resid 130 through 140 removed outlier: 4.249A pdb=" N ALA a 138 " --> pdb=" O GLN a 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 141 through 144 Processing helix chain 'a' and resid 160 through 177 removed outlier: 3.774A pdb=" N GLN a 173 " --> pdb=" O GLN a 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS a 174 " --> pdb=" O ARG a 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 15 Processing helix chain 'b' and resid 21 through 39 removed outlier: 3.973A pdb=" N LEU b 25 " --> pdb=" O ILE b 21 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE b 28 " --> pdb=" O PRO b 24 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU b 29 " --> pdb=" O LEU b 25 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'b' and resid 44 through 66 Proline residue: b 51 - end of helix Processing helix chain 'b' and resid 67 through 70 Processing helix chain 'b' and resid 71 through 77 removed outlier: 4.126A pdb=" N GLN b 75 " --> pdb=" O ARG b 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP b 76 " --> pdb=" O ASP b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 84 removed outlier: 3.901A pdb=" N GLN b 81 " --> pdb=" O GLY b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 119 removed outlier: 3.717A pdb=" N MET b 102 " --> pdb=" O MET b 98 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL b 103 " --> pdb=" O ALA b 99 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR b 104 " --> pdb=" O HIS b 100 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU b 106 " --> pdb=" O MET b 102 " (cutoff:3.500A) Proline residue: b 107 - end of helix Proline residue: b 113 - end of helix Processing helix chain 'b' and resid 122 through 152 removed outlier: 4.017A pdb=" N LEU b 135 " --> pdb=" O LEU b 131 " (cutoff:3.500A) Proline residue: b 138 - end of helix Proline residue: b 146 - end of helix Processing helix chain 'b' and resid 159 through 165 removed outlier: 3.630A pdb=" N SER b 162 " --> pdb=" O VAL b 159 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 183 Processing helix chain 'b' and resid 189 through 219 removed outlier: 3.692A pdb=" N ILE b 195 " --> pdb=" O GLY b 191 " (cutoff:3.500A) Proline residue: b 208 - end of helix removed outlier: 3.643A pdb=" N ALA b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 5.453A pdb=" N ALA A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 61 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLU A 8 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU A 59 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 6.257A pdb=" N LEU A 79 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP A 153 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 81 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 32 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TRP A 31 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE A 199 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 33 " --> pdb=" O ILE A 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 16 through 26 removed outlier: 5.610A pdb=" N THR a 17 " --> pdb=" O ARG a 13 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG a 13 " --> pdb=" O THR a 17 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE a 19 " --> pdb=" O CYS a 11 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU a 9 " --> pdb=" O GLY a 21 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER a 23 " --> pdb=" O ARG a 7 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG a 7 " --> pdb=" O SER a 23 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR a 25 " --> pdb=" O GLU a 5 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU a 5 " --> pdb=" O THR a 25 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU a 9 " --> pdb=" O ALA a 57 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA a 57 " --> pdb=" O LEU a 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 78 through 81 removed outlier: 6.202A pdb=" N LEU a 79 " --> pdb=" O ILE a 151 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASP a 153 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE a 81 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR a 184 " --> pdb=" O LEU a 152 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU a 30 " --> pdb=" O VAL a 181 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU a 183 " --> pdb=" O GLU a 30 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL a 32 " --> pdb=" O LEU a 183 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG a 197 " --> pdb=" O TRP a 31 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2092 1.33 - 1.46: 1941 1.46 - 1.58: 5071 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 9185 Sorted by residual: bond pdb=" C ILE B 170 " pdb=" N PRO B 171 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.36e-02 5.41e+03 1.76e+01 bond pdb=" C THR B 137 " pdb=" N PRO B 138 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.36e-02 5.41e+03 1.25e+01 bond pdb=" CA ARG b 12 " pdb=" C ARG b 12 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.37e-02 5.33e+03 9.64e+00 bond pdb=" C ARG b 12 " pdb=" N VAL b 13 " ideal model delta sigma weight residual 1.335 1.303 0.031 1.15e-02 7.56e+03 7.28e+00 bond pdb=" CA ILE D 30 " pdb=" CB ILE D 30 " ideal model delta sigma weight residual 1.539 1.526 0.013 5.40e-03 3.43e+04 5.60e+00 ... (remaining 9180 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 12200 3.09 - 6.18: 267 6.18 - 9.27: 59 9.27 - 12.36: 4 12.36 - 15.45: 1 Bond angle restraints: 12531 Sorted by residual: angle pdb=" N PHE C 209 " pdb=" CA PHE C 209 " pdb=" C PHE C 209 " ideal model delta sigma weight residual 111.14 104.49 6.65 1.08e+00 8.57e-01 3.79e+01 angle pdb=" CA GLU A 15 " pdb=" CB GLU A 15 " pdb=" CG GLU A 15 " ideal model delta sigma weight residual 114.10 124.93 -10.83 2.00e+00 2.50e-01 2.93e+01 angle pdb=" N GLU D 57 " pdb=" CA GLU D 57 " pdb=" CB GLU D 57 " ideal model delta sigma weight residual 110.41 118.70 -8.29 1.68e+00 3.54e-01 2.43e+01 angle pdb=" C ARG a 102 " pdb=" CA ARG a 102 " pdb=" CB ARG a 102 " ideal model delta sigma weight residual 117.23 110.56 6.67 1.36e+00 5.41e-01 2.40e+01 angle pdb=" CA MET b 129 " pdb=" CB MET b 129 " pdb=" CG MET b 129 " ideal model delta sigma weight residual 114.10 123.85 -9.75 2.00e+00 2.50e-01 2.38e+01 ... (remaining 12526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.42: 4868 18.42 - 36.85: 426 36.85 - 55.27: 86 55.27 - 73.69: 7 73.69 - 92.11: 6 Dihedral angle restraints: 5393 sinusoidal: 2102 harmonic: 3291 Sorted by residual: dihedral pdb=" CA HIS C 60 " pdb=" C HIS C 60 " pdb=" N VAL C 61 " pdb=" CA VAL C 61 " ideal model delta harmonic sigma weight residual -180.00 -157.68 -22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLN b 81 " pdb=" C GLN b 81 " pdb=" N LEU b 82 " pdb=" CA LEU b 82 " ideal model delta harmonic sigma weight residual 180.00 158.77 21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU b 154 " pdb=" C LEU b 154 " pdb=" N LYS b 155 " pdb=" CA LYS b 155 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 5390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1127 0.055 - 0.110: 267 0.110 - 0.165: 71 0.165 - 0.220: 13 0.220 - 0.275: 4 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA GLU A 15 " pdb=" N GLU A 15 " pdb=" C GLU A 15 " pdb=" CB GLU A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE C 57 " pdb=" CA ILE C 57 " pdb=" CG1 ILE C 57 " pdb=" CG2 ILE C 57 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1479 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 128 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ARG C 128 " 0.059 2.00e-02 2.50e+03 pdb=" O ARG C 128 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU C 129 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 50 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 51 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 15 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" CD GLU A 15 " 0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU A 15 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 15 " -0.018 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1796 2.78 - 3.31: 8679 3.31 - 3.84: 14544 3.84 - 4.37: 16100 4.37 - 4.90: 27312 Nonbonded interactions: 68431 Sorted by model distance: nonbonded pdb=" ND2 ASN C 223 " pdb=" OE1 GLN D 42 " model vdw 2.254 3.120 nonbonded pdb=" O MET A 171 " pdb=" OG1 THR A 175 " model vdw 2.272 3.040 nonbonded pdb=" O PHE B 142 " pdb=" OG SER B 207 " model vdw 2.338 3.040 nonbonded pdb=" NH1 ARG a 135 " pdb=" OG1 THR a 157 " model vdw 2.362 3.120 nonbonded pdb=" N GLN C 50 " pdb=" OE1 GLN C 50 " model vdw 2.381 3.120 ... (remaining 68426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.050 Set scattering table: 0.010 Process input model: 8.050 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9185 Z= 0.258 Angle : 1.112 15.454 12531 Z= 0.570 Chirality : 0.054 0.275 1482 Planarity : 0.008 0.084 1557 Dihedral : 14.353 92.115 3265 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.24), residues: 1141 helix: -0.52 (0.19), residues: 689 sheet: -0.60 (0.84), residues: 44 loop : -1.41 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 54 TYR 0.027 0.002 TYR C 58 PHE 0.036 0.002 PHE a 19 TRP 0.022 0.002 TRP b 55 HIS 0.007 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 9185) covalent geometry : angle 1.11168 (12531) hydrogen bonds : bond 0.13486 ( 496) hydrogen bonds : angle 5.94017 ( 1449) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8515 (mt) cc_final: 0.8268 (mp) REVERT: D 50 VAL cc_start: 0.8388 (t) cc_final: 0.8183 (t) REVERT: a 5 GLU cc_start: 0.7378 (pp20) cc_final: 0.6929 (pp20) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.0772 time to fit residues: 31.9229 Evaluate side-chains 239 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 133 GLN A 154 GLN A 186 HIS ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 90 ASN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 HIS ** a 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.096793 restraints weight = 16582.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099945 restraints weight = 9804.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.102047 restraints weight = 7047.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103354 restraints weight = 5712.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104313 restraints weight = 5016.344| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9185 Z= 0.219 Angle : 0.791 10.399 12531 Z= 0.388 Chirality : 0.045 0.195 1482 Planarity : 0.006 0.063 1557 Dihedral : 5.140 18.960 1236 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.85 % Allowed : 15.20 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.25), residues: 1141 helix: 0.43 (0.20), residues: 697 sheet: 0.30 (0.92), residues: 44 loop : -1.24 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.015 0.002 TYR A 100 PHE 0.026 0.002 PHE B 28 TRP 0.034 0.002 TRP C 66 HIS 0.007 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 9185) covalent geometry : angle 0.79115 (12531) hydrogen bonds : bond 0.04853 ( 496) hydrogen bonds : angle 4.96368 ( 1449) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.7836 (mtp) cc_final: 0.7635 (mtm) REVERT: B 192 TYR cc_start: 0.7461 (m-10) cc_final: 0.6973 (m-10) REVERT: C 50 GLN cc_start: 0.7511 (pm20) cc_final: 0.6924 (pm20) REVERT: C 54 TYR cc_start: 0.7891 (t80) cc_final: 0.7463 (t80) REVERT: a 30 GLU cc_start: 0.7599 (tp30) cc_final: 0.7398 (tp30) REVERT: b 72 ASP cc_start: 0.8472 (t0) cc_final: 0.7970 (t0) outliers start: 36 outliers final: 25 residues processed: 278 average time/residue: 0.0793 time to fit residues: 31.4285 Evaluate side-chains 273 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 248 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 145 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 187 GLN ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 HIS a 186 HIS a 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091633 restraints weight = 16874.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.094562 restraints weight = 10041.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096221 restraints weight = 7282.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097617 restraints weight = 6023.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098578 restraints weight = 5319.140| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 9185 Z= 0.242 Angle : 0.805 8.925 12531 Z= 0.395 Chirality : 0.046 0.214 1482 Planarity : 0.006 0.056 1557 Dihedral : 5.054 19.666 1236 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.57 % Allowed : 18.63 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.25), residues: 1141 helix: 0.75 (0.20), residues: 704 sheet: 0.31 (0.94), residues: 44 loop : -1.25 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 135 TYR 0.016 0.002 TYR C 58 PHE 0.026 0.002 PHE B 28 TRP 0.041 0.002 TRP C 66 HIS 0.008 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 9185) covalent geometry : angle 0.80450 (12531) hydrogen bonds : bond 0.05031 ( 496) hydrogen bonds : angle 4.85515 ( 1449) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8142 (mm-30) REVERT: B 131 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8787 (tt) REVERT: B 192 TYR cc_start: 0.7830 (m-10) cc_final: 0.7442 (m-10) REVERT: C 12 PRO cc_start: 0.8011 (Cg_endo) cc_final: 0.7527 (Cg_exo) REVERT: C 50 GLN cc_start: 0.8120 (pm20) cc_final: 0.7667 (pm20) REVERT: C 54 TYR cc_start: 0.8081 (t80) cc_final: 0.7844 (t80) REVERT: a 15 GLU cc_start: 0.7481 (pp20) cc_final: 0.7230 (pp20) REVERT: a 95 GLU cc_start: 0.8672 (tp30) cc_final: 0.8433 (tp30) REVERT: b 20 GLU cc_start: 0.9200 (tp30) cc_final: 0.8990 (tp30) REVERT: b 26 TRP cc_start: 0.7974 (m100) cc_final: 0.7762 (m100) REVERT: b 42 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7881 (tm-30) REVERT: b 72 ASP cc_start: 0.8858 (t0) cc_final: 0.8470 (t0) REVERT: b 117 MET cc_start: 0.8817 (tmm) cc_final: 0.8355 (mmp) outliers start: 52 outliers final: 37 residues processed: 284 average time/residue: 0.0790 time to fit residues: 32.0729 Evaluate side-chains 286 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 56 ASP Chi-restraints excluded: chain a residue 145 THR Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 187 GLN b 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.095719 restraints weight = 16687.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098811 restraints weight = 9782.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101071 restraints weight = 7012.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102444 restraints weight = 5672.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103502 restraints weight = 4945.863| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9185 Z= 0.136 Angle : 0.711 8.850 12531 Z= 0.342 Chirality : 0.042 0.216 1482 Planarity : 0.005 0.051 1557 Dihedral : 4.748 17.784 1236 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.60 % Allowed : 23.55 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.26), residues: 1141 helix: 1.19 (0.20), residues: 698 sheet: 0.25 (0.96), residues: 44 loop : -1.27 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 56 TYR 0.015 0.001 TYR C 48 PHE 0.026 0.001 PHE B 28 TRP 0.040 0.001 TRP C 234 HIS 0.004 0.001 HIS b 100 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9185) covalent geometry : angle 0.71149 (12531) hydrogen bonds : bond 0.04105 ( 496) hydrogen bonds : angle 4.43022 ( 1449) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 269 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 TYR cc_start: 0.7480 (m-10) cc_final: 0.7196 (m-10) REVERT: C 47 ASP cc_start: 0.8294 (t0) cc_final: 0.7887 (t0) REVERT: C 50 GLN cc_start: 0.8140 (pm20) cc_final: 0.7744 (pm20) REVERT: C 54 TYR cc_start: 0.8048 (t80) cc_final: 0.7817 (t80) REVERT: C 226 LEU cc_start: 0.8864 (mt) cc_final: 0.8441 (tt) REVERT: a 3 MET cc_start: 0.7155 (tpp) cc_final: 0.6929 (tpp) REVERT: a 11 CYS cc_start: 0.8591 (t) cc_final: 0.7099 (p) REVERT: a 95 GLU cc_start: 0.8603 (tp30) cc_final: 0.8382 (tp30) REVERT: a 189 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7281 (pp) REVERT: b 72 ASP cc_start: 0.8900 (t0) cc_final: 0.8475 (t0) outliers start: 43 outliers final: 27 residues processed: 285 average time/residue: 0.0833 time to fit residues: 33.5153 Evaluate side-chains 281 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 189 LEU Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 128 GLN b 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.090160 restraints weight = 17150.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.092970 restraints weight = 10521.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.094787 restraints weight = 7774.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.096078 restraints weight = 6434.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.096996 restraints weight = 5690.460| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 9185 Z= 0.279 Angle : 0.848 8.344 12531 Z= 0.411 Chirality : 0.048 0.238 1482 Planarity : 0.005 0.055 1557 Dihedral : 4.906 17.997 1236 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.89 % Allowed : 23.23 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.25), residues: 1141 helix: 0.89 (0.20), residues: 715 sheet: 0.14 (0.95), residues: 44 loop : -1.36 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 13 TYR 0.013 0.002 TYR A 100 PHE 0.025 0.002 PHE B 28 TRP 0.049 0.002 TRP C 234 HIS 0.008 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00672 ( 9185) covalent geometry : angle 0.84766 (12531) hydrogen bonds : bond 0.05103 ( 496) hydrogen bonds : angle 4.83054 ( 1449) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 260 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9544 (pt) cc_final: 0.9232 (pp) REVERT: B 10 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8155 (mm-30) REVERT: B 192 TYR cc_start: 0.7986 (m-10) cc_final: 0.7696 (m-10) REVERT: C 50 GLN cc_start: 0.8166 (pm20) cc_final: 0.7341 (pm20) REVERT: C 54 TYR cc_start: 0.8236 (t80) cc_final: 0.8016 (t80) REVERT: C 226 LEU cc_start: 0.9003 (mt) cc_final: 0.8747 (tt) REVERT: a 11 CYS cc_start: 0.8739 (t) cc_final: 0.7420 (p) REVERT: a 165 ASP cc_start: 0.8512 (p0) cc_final: 0.8311 (p0) REVERT: a 193 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7169 (tm-30) REVERT: b 26 TRP cc_start: 0.8154 (m100) cc_final: 0.7856 (m100) REVERT: b 72 ASP cc_start: 0.8978 (t0) cc_final: 0.8612 (t0) outliers start: 55 outliers final: 40 residues processed: 288 average time/residue: 0.0751 time to fit residues: 31.6184 Evaluate side-chains 285 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 38 SER Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS C 147 HIS b 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094761 restraints weight = 16698.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097866 restraints weight = 9909.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100017 restraints weight = 7150.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101386 restraints weight = 5813.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102402 restraints weight = 5098.144| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9185 Z= 0.142 Angle : 0.746 9.392 12531 Z= 0.357 Chirality : 0.042 0.240 1482 Planarity : 0.005 0.056 1557 Dihedral : 4.688 18.528 1236 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.18 % Allowed : 26.98 % Favored : 68.84 % 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 aren not related in a simple way. whole: 0.50 (0.26), residues: 1141 helix: 1.23 (0.20), residues: 713 sheet: 0.19 (0.95), residues: 44 loop : -1.36 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 56 TYR 0.009 0.001 TYR C 139 PHE 0.028 0.001 PHE B 28 TRP 0.040 0.002 TRP C 66 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9185) covalent geometry : angle 0.74606 (12531) hydrogen bonds : bond 0.04148 ( 496) hydrogen bonds : angle 4.42283 ( 1449) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9570 (pt) cc_final: 0.9266 (pp) REVERT: C 66 TRP cc_start: 0.8885 (m100) cc_final: 0.8578 (m100) REVERT: C 226 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8581 (tt) REVERT: a 11 CYS cc_start: 0.8586 (t) cc_final: 0.7272 (p) REVERT: a 95 GLU cc_start: 0.8575 (tp30) cc_final: 0.8356 (tp30) REVERT: a 165 ASP cc_start: 0.8447 (p0) cc_final: 0.8229 (p0) REVERT: a 193 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6931 (tm-30) REVERT: b 72 ASP cc_start: 0.9038 (t0) cc_final: 0.8687 (t0) REVERT: b 129 MET cc_start: 0.8158 (tpt) cc_final: 0.7934 (tpt) outliers start: 39 outliers final: 29 residues processed: 280 average time/residue: 0.0754 time to fit residues: 30.7700 Evaluate side-chains 280 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 189 LEU Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 83 MET Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 152 VAL Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.0070 chunk 67 optimal weight: 0.2980 chunk 78 optimal weight: 7.9990 chunk 52 optimal weight: 0.0470 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN b 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096779 restraints weight = 16810.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.100015 restraints weight = 9897.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102186 restraints weight = 7080.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103720 restraints weight = 5731.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104566 restraints weight = 4977.661| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9185 Z= 0.133 Angle : 0.735 9.530 12531 Z= 0.348 Chirality : 0.043 0.257 1482 Planarity : 0.005 0.056 1557 Dihedral : 4.513 18.049 1236 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.39 % Allowed : 27.19 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1141 helix: 1.38 (0.20), residues: 705 sheet: 0.25 (0.94), residues: 44 loop : -1.30 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 56 TYR 0.016 0.001 TYR C 48 PHE 0.030 0.001 PHE B 28 TRP 0.039 0.001 TRP C 66 HIS 0.004 0.000 HIS b 100 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9185) covalent geometry : angle 0.73545 (12531) hydrogen bonds : bond 0.03785 ( 496) hydrogen bonds : angle 4.27238 ( 1449) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9588 (pt) cc_final: 0.9273 (pp) REVERT: B 20 GLU cc_start: 0.8913 (tp30) cc_final: 0.8571 (mm-30) REVERT: C 50 GLN cc_start: 0.8476 (pm20) cc_final: 0.8146 (pm20) REVERT: C 66 TRP cc_start: 0.8821 (m100) cc_final: 0.8592 (m100) REVERT: C 226 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8658 (tt) REVERT: a 11 CYS cc_start: 0.8595 (t) cc_final: 0.7465 (p) REVERT: a 95 GLU cc_start: 0.8598 (tp30) cc_final: 0.8378 (tp30) REVERT: a 165 ASP cc_start: 0.8437 (p0) cc_final: 0.8219 (p0) REVERT: a 193 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6824 (tm-30) REVERT: b 72 ASP cc_start: 0.9077 (t0) cc_final: 0.8725 (t0) REVERT: b 117 MET cc_start: 0.8816 (tmm) cc_final: 0.8244 (mmp) outliers start: 41 outliers final: 28 residues processed: 283 average time/residue: 0.0760 time to fit residues: 31.5881 Evaluate side-chains 282 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 253 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 60 VAL Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 189 LEU Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 102 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN b 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093004 restraints weight = 17061.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.095989 restraints weight = 10367.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098051 restraints weight = 7572.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099450 restraints weight = 6185.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100155 restraints weight = 5419.316| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9185 Z= 0.193 Angle : 0.787 8.095 12531 Z= 0.375 Chirality : 0.045 0.284 1482 Planarity : 0.005 0.057 1557 Dihedral : 4.557 18.589 1236 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.03 % Allowed : 28.16 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.26), residues: 1141 helix: 1.30 (0.20), residues: 711 sheet: 0.26 (0.93), residues: 44 loop : -1.39 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 56 TYR 0.011 0.001 TYR A 100 PHE 0.027 0.001 PHE B 28 TRP 0.044 0.002 TRP C 234 HIS 0.004 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 9185) covalent geometry : angle 0.78748 (12531) hydrogen bonds : bond 0.04227 ( 496) hydrogen bonds : angle 4.45999 ( 1449) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9578 (pt) cc_final: 0.9260 (pp) REVERT: B 20 GLU cc_start: 0.8989 (tp30) cc_final: 0.8621 (mm-30) REVERT: C 50 GLN cc_start: 0.8557 (pm20) cc_final: 0.8155 (pm20) REVERT: C 66 TRP cc_start: 0.8850 (m100) cc_final: 0.8637 (m100) REVERT: C 226 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8765 (tt) REVERT: a 11 CYS cc_start: 0.8603 (t) cc_final: 0.7364 (p) REVERT: a 95 GLU cc_start: 0.8609 (tp30) cc_final: 0.8398 (tp30) REVERT: a 165 ASP cc_start: 0.8394 (p0) cc_final: 0.8160 (p0) REVERT: a 193 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6778 (tm-30) REVERT: b 26 TRP cc_start: 0.8178 (m100) cc_final: 0.7651 (m100) REVERT: b 72 ASP cc_start: 0.9120 (t0) cc_final: 0.8801 (t0) REVERT: b 109 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7772 (mp) REVERT: b 117 MET cc_start: 0.8792 (tmm) cc_final: 0.8222 (mmp) outliers start: 47 outliers final: 38 residues processed: 271 average time/residue: 0.0815 time to fit residues: 32.2105 Evaluate side-chains 285 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 35 THR Chi-restraints excluded: chain a residue 60 VAL Chi-restraints excluded: chain a residue 68 HIS Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 189 LEU Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 100 HIS Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 164 LEU Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN a 63 GLN b 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.096070 restraints weight = 16699.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099261 restraints weight = 9918.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101463 restraints weight = 7117.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102714 restraints weight = 5746.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103787 restraints weight = 5041.930| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9185 Z= 0.143 Angle : 0.775 11.408 12531 Z= 0.366 Chirality : 0.043 0.297 1482 Planarity : 0.005 0.056 1557 Dihedral : 4.545 37.378 1236 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.39 % Allowed : 28.91 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1141 helix: 1.40 (0.20), residues: 715 sheet: 0.18 (0.91), residues: 44 loop : -1.43 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 47 TYR 0.015 0.001 TYR C 48 PHE 0.030 0.001 PHE B 28 TRP 0.042 0.001 TRP C 66 HIS 0.004 0.000 HIS b 100 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9185) covalent geometry : angle 0.77546 (12531) hydrogen bonds : bond 0.03809 ( 496) hydrogen bonds : angle 4.30396 ( 1449) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9584 (pt) cc_final: 0.9283 (pp) REVERT: B 20 GLU cc_start: 0.8998 (tp30) cc_final: 0.8590 (mm-30) REVERT: C 50 GLN cc_start: 0.8553 (pm20) cc_final: 0.8215 (pm20) REVERT: C 66 TRP cc_start: 0.8849 (m100) cc_final: 0.8610 (m100) REVERT: C 226 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8599 (tt) REVERT: a 11 CYS cc_start: 0.8591 (t) cc_final: 0.7268 (p) REVERT: a 95 GLU cc_start: 0.8619 (tp30) cc_final: 0.8395 (tp30) REVERT: a 165 ASP cc_start: 0.8391 (p0) cc_final: 0.8167 (p0) REVERT: a 193 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6885 (tm-30) REVERT: a 195 LYS cc_start: 0.8612 (ptpp) cc_final: 0.8376 (ptpp) REVERT: b 72 ASP cc_start: 0.9113 (t0) cc_final: 0.8788 (t0) REVERT: b 117 MET cc_start: 0.8823 (tmm) cc_final: 0.8216 (mmp) outliers start: 41 outliers final: 34 residues processed: 279 average time/residue: 0.0821 time to fit residues: 33.3762 Evaluate side-chains 294 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 60 VAL Chi-restraints excluded: chain a residue 68 HIS Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 145 THR Chi-restraints excluded: chain a residue 189 LEU Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 100 HIS Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.096354 restraints weight = 16644.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099476 restraints weight = 10002.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101541 restraints weight = 7229.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102990 restraints weight = 5889.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103835 restraints weight = 5151.403| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9185 Z= 0.142 Angle : 0.791 14.216 12531 Z= 0.371 Chirality : 0.044 0.317 1482 Planarity : 0.005 0.057 1557 Dihedral : 4.459 28.515 1236 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.75 % Allowed : 29.98 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1141 helix: 1.44 (0.20), residues: 715 sheet: 0.22 (0.91), residues: 44 loop : -1.47 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 56 TYR 0.009 0.001 TYR A 100 PHE 0.029 0.001 PHE B 28 TRP 0.046 0.002 TRP C 234 HIS 0.004 0.001 HIS b 100 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9185) covalent geometry : angle 0.79109 (12531) hydrogen bonds : bond 0.03741 ( 496) hydrogen bonds : angle 4.24316 ( 1449) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9579 (pt) cc_final: 0.9270 (pp) REVERT: A 173 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: B 20 GLU cc_start: 0.8961 (tp30) cc_final: 0.8555 (mm-30) REVERT: C 50 GLN cc_start: 0.8551 (pm20) cc_final: 0.8226 (pm20) REVERT: C 58 TYR cc_start: 0.7923 (m-80) cc_final: 0.7629 (m-80) REVERT: C 66 TRP cc_start: 0.8863 (m100) cc_final: 0.8610 (m100) REVERT: C 226 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8608 (tt) REVERT: a 95 GLU cc_start: 0.8607 (tp30) cc_final: 0.8385 (tp30) REVERT: a 165 ASP cc_start: 0.8372 (p0) cc_final: 0.8146 (p0) REVERT: a 193 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6839 (tm-30) REVERT: a 195 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8401 (ptpp) REVERT: b 72 ASP cc_start: 0.9113 (t0) cc_final: 0.8805 (t0) REVERT: b 117 MET cc_start: 0.8810 (tmm) cc_final: 0.8201 (mmp) REVERT: b 123 VAL cc_start: 0.8911 (m) cc_final: 0.8632 (t) outliers start: 35 outliers final: 31 residues processed: 284 average time/residue: 0.0809 time to fit residues: 33.4202 Evaluate side-chains 291 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 258 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 60 VAL Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 145 THR Chi-restraints excluded: chain a residue 189 LEU Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 56 VAL Chi-restraints excluded: chain b residue 100 HIS Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 139 THR Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS b 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.092722 restraints weight = 16942.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095711 restraints weight = 10274.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097739 restraints weight = 7510.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099155 restraints weight = 6175.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.099873 restraints weight = 5405.383| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9185 Z= 0.197 Angle : 0.838 13.007 12531 Z= 0.395 Chirality : 0.046 0.325 1482 Planarity : 0.005 0.056 1557 Dihedral : 4.584 42.566 1236 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.28 % Allowed : 29.66 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.26), residues: 1141 helix: 1.36 (0.20), residues: 711 sheet: 0.40 (0.91), residues: 44 loop : -1.48 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 56 TYR 0.012 0.001 TYR A 100 PHE 0.027 0.001 PHE B 28 TRP 0.045 0.002 TRP C 234 HIS 0.021 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9185) covalent geometry : angle 0.83780 (12531) hydrogen bonds : bond 0.04272 ( 496) hydrogen bonds : angle 4.43082 ( 1449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.99 seconds wall clock time: 28 minutes 42.82 seconds (1722.82 seconds total)