Starting phenix.real_space_refine on Mon May 12 05:22:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cea_16602/05_2025/8cea_16602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cea_16602/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cea_16602/05_2025/8cea_16602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cea_16602/05_2025/8cea_16602.map" model { file = "/net/cci-nas-00/data/ceres_data/8cea_16602/05_2025/8cea_16602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cea_16602/05_2025/8cea_16602.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.27, per 1000 atoms: 0.59 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.80 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: 2.13 Time building geometry restraints manager: 2.51 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.500 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.002 TRP b 55 HIS 0.007 0.001 HIS A 174 PHE 0.036 0.002 PHE a 19 TYR 0.027 0.002 TYR C 58 ARG 0.008 0.001 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.13486 ( 496) hydrogen bonds : angle 5.94017 ( 1449) covalent geometry : bond 0.00507 ( 9185) covalent geometry : angle 1.11168 (12531) *********************** 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 : 0.917 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: 0.1841 time to fit residues: 75.6320 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 : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 65 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 C 6 HIS ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105344 restraints weight = 16397.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108750 restraints weight = 9753.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111097 restraints weight = 6981.338| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9185 Z= 0.136 Angle : 0.725 9.954 12531 Z= 0.351 Chirality : 0.042 0.193 1482 Planarity : 0.006 0.061 1557 Dihedral : 5.054 17.952 1236 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.78 % Allowed : 12.96 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1141 helix: 0.47 (0.20), residues: 695 sheet: 0.23 (0.90), residues: 44 loop : -1.41 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 66 HIS 0.004 0.001 HIS A 174 PHE 0.027 0.001 PHE B 28 TYR 0.012 0.001 TYR A 100 ARG 0.003 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 496) hydrogen bonds : angle 4.78930 ( 1449) covalent geometry : bond 0.00299 ( 9185) covalent geometry : angle 0.72452 (12531) *********************** 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 296 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8900 (mt) cc_final: 0.8531 (tt) REVERT: B 83 MET cc_start: 0.7544 (mtp) cc_final: 0.7052 (mtm) REVERT: C 54 TYR cc_start: 0.7740 (t80) cc_final: 0.7339 (t80) REVERT: a 30 GLU cc_start: 0.7571 (tp30) cc_final: 0.7356 (tp30) REVERT: a 195 LYS cc_start: 0.8352 (ptpp) cc_final: 0.8136 (ptpp) REVERT: b 72 ASP cc_start: 0.8442 (t0) cc_final: 0.8213 (t0) outliers start: 26 outliers final: 15 residues processed: 277 average time/residue: 0.1890 time to fit residues: 73.2755 Evaluate side-chains 263 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 248 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 219 ILE 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 40 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS C 85 GLN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102567 restraints weight = 16499.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105936 restraints weight = 9691.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108284 restraints weight = 6909.686| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9185 Z= 0.132 Angle : 0.677 8.229 12531 Z= 0.329 Chirality : 0.042 0.199 1482 Planarity : 0.005 0.054 1557 Dihedral : 4.751 17.815 1236 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.53 % Allowed : 17.99 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1141 helix: 0.96 (0.20), residues: 690 sheet: 0.40 (0.92), residues: 44 loop : -1.27 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 66 HIS 0.004 0.001 HIS A 174 PHE 0.024 0.001 PHE B 28 TYR 0.015 0.001 TYR C 48 ARG 0.003 0.000 ARG D 54 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 496) hydrogen bonds : angle 4.54543 ( 1449) covalent geometry : bond 0.00299 ( 9185) covalent geometry : angle 0.67672 (12531) *********************** 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 289 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: B 5 ARG cc_start: 0.8908 (tpp80) cc_final: 0.8664 (tpp80) REVERT: B 83 MET cc_start: 0.7733 (mtp) cc_final: 0.7504 (mtm) REVERT: C 47 ASP cc_start: 0.8055 (t0) cc_final: 0.7759 (t0) REVERT: C 54 TYR cc_start: 0.7777 (t80) cc_final: 0.7544 (t80) REVERT: D 54 ARG cc_start: 0.8996 (tmt-80) cc_final: 0.8341 (tpp-160) REVERT: a 195 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8196 (ptpp) REVERT: b 72 ASP cc_start: 0.8591 (t0) cc_final: 0.8321 (t0) REVERT: b 117 MET cc_start: 0.8833 (tmm) cc_final: 0.8385 (mmp) outliers start: 33 outliers final: 21 residues processed: 266 average time/residue: 0.2034 time to fit residues: 75.1938 Evaluate side-chains 270 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 15 PHE Chi-restraints excluded: chain B residue 21 ILE 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 170 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 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 = 0.3647 r_free = 0.3647 target = 0.131663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.101497 restraints weight = 16518.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104890 restraints weight = 9644.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107003 restraints weight = 6860.978| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9185 Z= 0.135 Angle : 0.686 9.049 12531 Z= 0.331 Chirality : 0.042 0.211 1482 Planarity : 0.005 0.053 1557 Dihedral : 4.608 17.935 1236 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.39 % Allowed : 19.06 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1141 helix: 1.19 (0.20), residues: 697 sheet: 0.62 (0.94), residues: 44 loop : -1.25 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 234 HIS 0.004 0.001 HIS A 174 PHE 0.025 0.001 PHE B 28 TYR 0.010 0.001 TYR A 100 ARG 0.003 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 496) hydrogen bonds : angle 4.39104 ( 1449) covalent geometry : bond 0.00313 ( 9185) covalent geometry : angle 0.68641 (12531) *********************** 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 293 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 83 MET cc_start: 0.7894 (mtp) cc_final: 0.7670 (mtm) REVERT: C 50 GLN cc_start: 0.7911 (pm20) cc_final: 0.7427 (pm20) REVERT: C 54 TYR cc_start: 0.7735 (t80) cc_final: 0.7507 (t80) REVERT: a 3 MET cc_start: 0.7210 (tpp) cc_final: 0.6845 (tpp) REVERT: a 30 GLU cc_start: 0.7422 (tp30) cc_final: 0.7212 (tp30) REVERT: a 95 GLU cc_start: 0.8547 (tp30) cc_final: 0.8156 (tp30) REVERT: b 72 ASP cc_start: 0.8724 (t0) cc_final: 0.8352 (t0) REVERT: b 81 GLN cc_start: 0.8648 (mt0) cc_final: 0.8380 (mt0) outliers start: 41 outliers final: 28 residues processed: 263 average time/residue: 0.1923 time to fit residues: 69.9607 Evaluate side-chains 272 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 15 PHE 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 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 215 LEU Chi-restraints excluded: chain B residue 219 ILE 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 27 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain b residue 35 PHE Chi-restraints excluded: chain b residue 37 LEU Chi-restraints excluded: chain b residue 85 LEU Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 1.9990 chunk 85 optimal weight: 0.0870 chunk 41 optimal weight: 0.3980 chunk 19 optimal weight: 0.0040 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 43 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 overall best weight: 0.3088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103036 restraints weight = 16406.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106512 restraints weight = 9410.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108926 restraints weight = 6638.756| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9185 Z= 0.131 Angle : 0.682 10.846 12531 Z= 0.327 Chirality : 0.041 0.231 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.525 18.525 1236 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.53 % Allowed : 20.34 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1141 helix: 1.36 (0.20), residues: 692 sheet: 0.68 (0.94), residues: 44 loop : -1.25 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 234 HIS 0.003 0.000 HIS b 100 PHE 0.027 0.001 PHE B 28 TYR 0.016 0.001 TYR C 48 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 496) hydrogen bonds : angle 4.25797 ( 1449) covalent geometry : bond 0.00282 ( 9185) covalent geometry : angle 0.68172 (12531) *********************** 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 295 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: B 83 MET cc_start: 0.7893 (mtp) cc_final: 0.7678 (mtm) REVERT: C 56 ILE cc_start: 0.8497 (mm) cc_final: 0.8296 (mm) REVERT: D 54 ARG cc_start: 0.9054 (tpt170) cc_final: 0.8320 (tpp-160) REVERT: a 3 MET cc_start: 0.7334 (tpp) cc_final: 0.7040 (tpp) REVERT: a 30 GLU cc_start: 0.7544 (tp30) cc_final: 0.7240 (tp30) REVERT: a 95 GLU cc_start: 0.8548 (tp30) cc_final: 0.8142 (tp30) REVERT: b 42 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7323 (tm-30) REVERT: b 72 ASP cc_start: 0.8789 (t0) cc_final: 0.8397 (t0) REVERT: b 81 GLN cc_start: 0.8599 (mt0) cc_final: 0.8222 (mt0) outliers start: 33 outliers final: 27 residues processed: 271 average time/residue: 0.1955 time to fit residues: 73.5611 Evaluate side-chains 277 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 15 PHE 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 170 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 180 ILE 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 131 LEU Chi-restraints excluded: chain b residue 150 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 186 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100387 restraints weight = 16403.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103720 restraints weight = 9523.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105933 restraints weight = 6747.182| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9185 Z= 0.143 Angle : 0.715 9.547 12531 Z= 0.343 Chirality : 0.043 0.253 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.480 17.869 1236 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.07 % Allowed : 21.41 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1141 helix: 1.38 (0.20), residues: 693 sheet: 0.73 (0.93), residues: 44 loop : -1.26 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 66 HIS 0.007 0.001 HIS A 68 PHE 0.028 0.001 PHE B 28 TYR 0.031 0.001 TYR A 100 ARG 0.006 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 496) hydrogen bonds : angle 4.28852 ( 1449) covalent geometry : bond 0.00338 ( 9185) covalent geometry : angle 0.71485 (12531) *********************** 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 300 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 171 MET cc_start: 0.8151 (mtp) cc_final: 0.7934 (mtm) REVERT: B 20 GLU cc_start: 0.8881 (tp30) cc_final: 0.8485 (mm-30) REVERT: C 50 GLN cc_start: 0.8273 (pm20) cc_final: 0.8056 (pm20) REVERT: C 96 MET cc_start: 0.8231 (mtm) cc_final: 0.7914 (mtm) REVERT: C 219 MET cc_start: 0.9251 (tmm) cc_final: 0.9021 (tmm) REVERT: C 226 LEU cc_start: 0.8698 (mt) cc_final: 0.8368 (tt) REVERT: D 54 ARG cc_start: 0.9057 (tpt170) cc_final: 0.8401 (tpp-160) REVERT: a 95 GLU cc_start: 0.8582 (tp30) cc_final: 0.8191 (tp30) REVERT: b 3 PHE cc_start: 0.8918 (t80) cc_final: 0.8688 (t80) REVERT: b 72 ASP cc_start: 0.8835 (t0) cc_final: 0.8472 (t0) REVERT: b 117 MET cc_start: 0.8860 (tmm) cc_final: 0.8337 (mmp) outliers start: 38 outliers final: 31 residues processed: 274 average time/residue: 0.2036 time to fit residues: 78.1986 Evaluate side-chains 273 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 B residue 15 PHE 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 170 ILE Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 70 ILE 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 57 GLU Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 181 VAL 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 131 LEU Chi-restraints excluded: chain b residue 150 LEU 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 45 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN D 53 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 = 0.3628 r_free = 0.3628 target = 0.129679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100001 restraints weight = 16801.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103244 restraints weight = 10105.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105338 restraints weight = 7252.124| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9185 Z= 0.153 Angle : 0.752 9.560 12531 Z= 0.361 Chirality : 0.043 0.216 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.504 24.689 1236 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.07 % Allowed : 22.06 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1141 helix: 1.39 (0.20), residues: 697 sheet: 0.69 (0.93), residues: 44 loop : -1.11 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 66 HIS 0.020 0.001 HIS A 68 PHE 0.028 0.001 PHE B 28 TYR 0.025 0.002 TYR A 100 ARG 0.004 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 496) hydrogen bonds : angle 4.33609 ( 1449) covalent geometry : bond 0.00366 ( 9185) covalent geometry : angle 0.75198 (12531) *********************** 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 300 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8987 (mm) cc_final: 0.8783 (mp) REVERT: A 144 LEU cc_start: 0.9566 (pt) cc_final: 0.9228 (pp) REVERT: A 171 MET cc_start: 0.8210 (mtp) cc_final: 0.7946 (mtm) REVERT: B 20 GLU cc_start: 0.8889 (tp30) cc_final: 0.8491 (mm-30) REVERT: B 122 ASP cc_start: 0.8382 (p0) cc_final: 0.7487 (p0) REVERT: B 129 MET cc_start: 0.8087 (tmm) cc_final: 0.7830 (tmm) REVERT: B 192 TYR cc_start: 0.7213 (m-10) cc_final: 0.6975 (m-10) REVERT: C 49 GLN cc_start: 0.8277 (mp10) cc_final: 0.7950 (tt0) REVERT: C 50 GLN cc_start: 0.8245 (pm20) cc_final: 0.7775 (pm20) REVERT: C 226 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8494 (tt) REVERT: D 54 ARG cc_start: 0.9120 (tpt170) cc_final: 0.8384 (tpp-160) REVERT: a 95 GLU cc_start: 0.8577 (tp30) cc_final: 0.8200 (tp30) REVERT: b 3 PHE cc_start: 0.8926 (t80) cc_final: 0.8678 (t80) REVERT: b 72 ASP cc_start: 0.8861 (t0) cc_final: 0.8516 (t0) REVERT: b 81 GLN cc_start: 0.8361 (mt0) cc_final: 0.8015 (mt0) REVERT: b 117 MET cc_start: 0.8815 (tmm) cc_final: 0.8274 (mmp) outliers start: 38 outliers final: 28 residues processed: 273 average time/residue: 0.1879 time to fit residues: 71.8171 Evaluate side-chains 278 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 35 PHE Chi-restraints excluded: chain B residue 37 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 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 215 LEU Chi-restraints excluded: chain C residue 25 LEU 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 226 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 181 VAL 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 131 LEU 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 99 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 54 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.131064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101518 restraints weight = 16711.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.104864 restraints weight = 9724.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107173 restraints weight = 6889.074| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9185 Z= 0.134 Angle : 0.734 8.910 12531 Z= 0.352 Chirality : 0.043 0.275 1482 Planarity : 0.005 0.051 1557 Dihedral : 4.427 19.256 1236 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.85 % Allowed : 23.23 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1141 helix: 1.42 (0.20), residues: 702 sheet: 0.66 (0.93), residues: 44 loop : -1.17 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 66 HIS 0.003 0.000 HIS A 174 PHE 0.029 0.001 PHE B 28 TYR 0.021 0.001 TYR A 100 ARG 0.003 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 496) hydrogen bonds : angle 4.26807 ( 1449) covalent geometry : bond 0.00307 ( 9185) covalent geometry : angle 0.73389 (12531) *********************** 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 292 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 0.960 Fit side-chains REVERT: A 144 LEU cc_start: 0.9586 (pt) cc_final: 0.9255 (pp) REVERT: A 171 MET cc_start: 0.8185 (mtp) cc_final: 0.7972 (mtm) REVERT: B 20 GLU cc_start: 0.8914 (tp30) cc_final: 0.8515 (mm-30) REVERT: B 122 ASP cc_start: 0.8386 (p0) cc_final: 0.7523 (p0) REVERT: B 129 MET cc_start: 0.8059 (tmm) cc_final: 0.7811 (tmm) REVERT: B 192 TYR cc_start: 0.7207 (m-10) cc_final: 0.6967 (m-10) REVERT: C 226 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8477 (tt) REVERT: D 54 ARG cc_start: 0.9095 (tpt170) cc_final: 0.8411 (tpp-160) REVERT: D 57 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6174 (pm20) REVERT: a 95 GLU cc_start: 0.8588 (tp30) cc_final: 0.8219 (tp30) REVERT: a 195 LYS cc_start: 0.8522 (ptpp) cc_final: 0.8313 (ptpp) REVERT: b 3 PHE cc_start: 0.8903 (t80) cc_final: 0.8696 (t80) REVERT: b 72 ASP cc_start: 0.8915 (t0) cc_final: 0.8556 (t0) REVERT: b 83 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8474 (ttm) REVERT: b 117 MET cc_start: 0.8788 (tmm) cc_final: 0.8248 (mmp) outliers start: 36 outliers final: 28 residues processed: 269 average time/residue: 0.2011 time to fit residues: 74.6732 Evaluate side-chains 272 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 176 GLU Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 37 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 195 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 50 THR Chi-restraints excluded: chain a residue 180 ILE Chi-restraints excluded: chain a residue 181 VAL 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 83 MET Chi-restraints excluded: chain b residue 131 LEU Chi-restraints excluded: chain b residue 150 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 71 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.129718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099975 restraints weight = 16771.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103075 restraints weight = 10104.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105242 restraints weight = 7345.164| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9185 Z= 0.153 Angle : 0.762 8.710 12531 Z= 0.365 Chirality : 0.044 0.337 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.453 23.863 1236 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.53 % Allowed : 23.88 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1141 helix: 1.42 (0.20), residues: 701 sheet: 0.60 (0.93), residues: 44 loop : -1.18 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP b 26 HIS 0.007 0.001 HIS A 68 PHE 0.029 0.001 PHE B 28 TYR 0.021 0.001 TYR A 100 ARG 0.003 0.000 ARG a 16 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 496) hydrogen bonds : angle 4.31969 ( 1449) covalent geometry : bond 0.00368 ( 9185) covalent geometry : angle 0.76198 (12531) *********************** 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 285 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.9583 (pt) cc_final: 0.9246 (pp) REVERT: A 171 MET cc_start: 0.8232 (mtp) cc_final: 0.7952 (mtm) REVERT: B 20 GLU cc_start: 0.8911 (tp30) cc_final: 0.8552 (mm-30) REVERT: B 122 ASP cc_start: 0.8446 (p0) cc_final: 0.7621 (p0) REVERT: B 129 MET cc_start: 0.8052 (tmm) cc_final: 0.7809 (tmm) REVERT: B 180 MET cc_start: 0.8098 (tmm) cc_final: 0.7828 (tmm) REVERT: B 192 TYR cc_start: 0.7308 (m-10) cc_final: 0.7056 (m-10) REVERT: C 50 GLN cc_start: 0.8318 (pm20) cc_final: 0.8041 (pm20) REVERT: C 226 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8528 (tt) REVERT: D 54 ARG cc_start: 0.9080 (tpt170) cc_final: 0.8336 (tpp-160) REVERT: a 95 GLU cc_start: 0.8590 (tp30) cc_final: 0.8243 (tp30) REVERT: a 195 LYS cc_start: 0.8580 (ptpp) cc_final: 0.8358 (ptpp) REVERT: b 72 ASP cc_start: 0.8885 (t0) cc_final: 0.8539 (t0) REVERT: b 83 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8496 (ttm) REVERT: b 126 TRP cc_start: 0.7553 (t60) cc_final: 0.7327 (t60) outliers start: 33 outliers final: 28 residues processed: 263 average time/residue: 0.1953 time to fit residues: 71.9398 Evaluate side-chains 276 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 176 GLU 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 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 195 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 50 THR 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 83 MET Chi-restraints excluded: chain b residue 131 LEU 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 100 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.1980 chunk 88 optimal weight: 9.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.128538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099195 restraints weight = 16710.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102266 restraints weight = 10034.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104389 restraints weight = 7254.842| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9185 Z= 0.162 Angle : 0.783 9.090 12531 Z= 0.374 Chirality : 0.045 0.331 1482 Planarity : 0.005 0.052 1557 Dihedral : 4.530 34.605 1236 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.43 % Allowed : 24.41 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1141 helix: 1.39 (0.20), residues: 708 sheet: 0.55 (0.93), residues: 44 loop : -1.33 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 66 HIS 0.012 0.001 HIS A 68 PHE 0.029 0.001 PHE B 28 TYR 0.021 0.002 TYR A 100 ARG 0.004 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 496) hydrogen bonds : angle 4.37811 ( 1449) covalent geometry : bond 0.00390 ( 9185) covalent geometry : angle 0.78288 (12531) ********************** 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 280 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8955 (mm) cc_final: 0.8709 (mp) REVERT: A 144 LEU cc_start: 0.9590 (pt) cc_final: 0.9261 (pp) REVERT: A 171 MET cc_start: 0.8215 (mtp) cc_final: 0.7974 (mtm) REVERT: B 20 GLU cc_start: 0.8932 (tp30) cc_final: 0.8554 (mm-30) REVERT: B 122 ASP cc_start: 0.8451 (p0) cc_final: 0.7964 (p0) REVERT: B 129 MET cc_start: 0.8081 (tmm) cc_final: 0.7833 (tmm) REVERT: B 180 MET cc_start: 0.8115 (tmm) cc_final: 0.7820 (tmm) REVERT: B 192 TYR cc_start: 0.7384 (m-10) cc_final: 0.7137 (m-10) REVERT: C 33 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7942 (tt) REVERT: C 48 TYR cc_start: 0.7543 (t80) cc_final: 0.7318 (t80) REVERT: C 49 GLN cc_start: 0.8306 (mp10) cc_final: 0.7567 (tm-30) REVERT: C 50 GLN cc_start: 0.8273 (pm20) cc_final: 0.7531 (pm20) REVERT: C 226 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8625 (tt) REVERT: D 54 ARG cc_start: 0.9086 (tpt170) cc_final: 0.8344 (tpp-160) REVERT: a 95 GLU cc_start: 0.8604 (tp30) cc_final: 0.8252 (tp30) REVERT: a 195 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8369 (ptpp) REVERT: b 72 ASP cc_start: 0.8920 (t0) cc_final: 0.8598 (t0) REVERT: b 117 MET cc_start: 0.8811 (tmm) cc_final: 0.8170 (mmp) REVERT: b 126 TRP cc_start: 0.7638 (t60) cc_final: 0.7378 (t60) outliers start: 32 outliers final: 24 residues processed: 258 average time/residue: 0.1905 time to fit residues: 68.0576 Evaluate side-chains 269 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 15 PHE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 37 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 195 ILE Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain a residue 50 THR 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 131 LEU 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 6 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099516 restraints weight = 16730.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102666 restraints weight = 9881.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104859 restraints weight = 7082.594| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9185 Z= 0.149 Angle : 0.774 9.959 12531 Z= 0.370 Chirality : 0.044 0.311 1482 Planarity : 0.005 0.051 1557 Dihedral : 4.525 40.408 1236 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.21 % Allowed : 24.63 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1141 helix: 1.39 (0.20), residues: 709 sheet: 0.54 (0.92), residues: 44 loop : -1.32 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 66 HIS 0.003 0.000 HIS A 174 PHE 0.030 0.001 PHE B 28 TYR 0.020 0.001 TYR A 100 ARG 0.004 0.000 ARG D 56 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 496) hydrogen bonds : angle 4.33797 ( 1449) covalent geometry : bond 0.00354 ( 9185) covalent geometry : angle 0.77394 (12531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3125.49 seconds wall clock time: 55 minutes 24.79 seconds (3324.79 seconds total)