Starting phenix.real_space_refine on Thu Mar 5 01:39:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tmj_10523/03_2026/6tmj_10523.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tmj_10523/03_2026/6tmj_10523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tmj_10523/03_2026/6tmj_10523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tmj_10523/03_2026/6tmj_10523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tmj_10523/03_2026/6tmj_10523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tmj_10523/03_2026/6tmj_10523.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 5771 2.51 5 N 1428 2.21 5 O 1641 1.98 5 H 9178 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18084 Number of models: 1 Model: "" Number of chains: 15 Chain: "Q" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 190 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Chain: "K" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1159 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "g2" Number of atoms: 3233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3233 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain: "d2" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2145 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "e2" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1077 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "H2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "I2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "J2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "K2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "M2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "N2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "O2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "P2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "Q2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "L2" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1028 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Time building chain proxies: 3.74, per 1000 atoms: 0.21 Number of scatterers: 18084 At special positions: 0 Unit cell: (93.79, 84.66, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 1641 8.00 N 1428 7.00 C 5771 6.00 H 9178 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 577.8 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 3 sheets defined 77.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'Q' and resid 9 through 14 removed outlier: 3.663A pdb=" N GLU Q 14 " --> pdb=" O SER Q 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 185 Proline residue: K 167 - end of helix removed outlier: 3.760A pdb=" N ALA K 170 " --> pdb=" O ARG K 166 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE K 174 " --> pdb=" O ALA K 170 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY K 175 " --> pdb=" O PHE K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 218 Processing helix chain 'g2' and resid 68 through 80 Processing helix chain 'g2' and resid 81 through 93 removed outlier: 3.814A pdb=" N ALAg2 85 " --> pdb=" O GLYg2 81 " (cutoff:3.500A) Proline residue: g2 87 - end of helix Processing helix chain 'g2' and resid 119 through 138 removed outlier: 3.547A pdb=" N METg2 137 " --> pdb=" O LYSg2 133 " (cutoff:3.500A) Processing helix chain 'g2' and resid 148 through 156 removed outlier: 3.958A pdb=" N ARGg2 152 " --> pdb=" O GLYg2 148 " (cutoff:3.500A) Processing helix chain 'g2' and resid 169 through 173 removed outlier: 3.551A pdb=" N ARGg2 172 " --> pdb=" O GLUg2 169 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHEg2 173 " --> pdb=" O VALg2 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'g2' and resid 169 through 173' Processing helix chain 'g2' and resid 177 through 190 removed outlier: 3.952A pdb=" N ILEg2 183 " --> pdb=" O GLNg2 179 " (cutoff:3.500A) Processing helix chain 'g2' and resid 217 through 223 removed outlier: 3.815A pdb=" N GLNg2 223 " --> pdb=" O THRg2 219 " (cutoff:3.500A) Processing helix chain 'g2' and resid 237 through 270 removed outlier: 5.299A pdb=" N LYSg2 243 " --> pdb=" O THRg2 239 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASPg2 244 " --> pdb=" O ASPg2 240 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASPg2 247 " --> pdb=" O LYSg2 243 " (cutoff:3.500A) Processing helix chain 'd2' and resid 142 through 158 removed outlier: 4.148A pdb=" N GLYd2 158 " --> pdb=" O GLNd2 154 " (cutoff:3.500A) Processing helix chain 'd2' and resid 161 through 182 Processing helix chain 'e2' and resid 1 through 6 Processing helix chain 'e2' and resid 8 through 23 removed outlier: 3.645A pdb=" N TYRe2 12 " --> pdb=" O SERe2 8 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEUe2 19 " --> pdb=" O GLUe2 15 " (cutoff:3.500A) Processing helix chain 'e2' and resid 25 through 36 removed outlier: 4.446A pdb=" N GLNe2 31 " --> pdb=" O PROe2 27 " (cutoff:3.500A) Processing helix chain 'e2' and resid 58 through 65 removed outlier: 3.516A pdb=" N ALAe2 62 " --> pdb=" O ASPe2 58 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALAe2 65 " --> pdb=" O LYSe2 61 " (cutoff:3.500A) Processing helix chain 'H2' and resid 97 through 107 removed outlier: 3.767A pdb=" N LEUH2 101 " --> pdb=" O GLYH2 97 " (cutoff:3.500A) Processing helix chain 'H2' and resid 109 through 131 removed outlier: 3.885A pdb=" N VALH2 113 " --> pdb=" O SERH2 109 " (cutoff:3.500A) Processing helix chain 'H2' and resid 134 through 166 removed outlier: 4.369A pdb=" N THRH2 140 " --> pdb=" O GLUH2 136 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THRH2 142 " --> pdb=" O LEUH2 138 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHEH2 148 " --> pdb=" O ILEH2 144 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHEH2 151 " --> pdb=" O GLYH2 147 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SERH2 160 " --> pdb=" O CYSH2 156 " (cutoff:3.500A) Processing helix chain 'I2' and resid 97 through 108 removed outlier: 3.600A pdb=" N LEUI2 101 " --> pdb=" O GLYI2 97 " (cutoff:3.500A) Processing helix chain 'I2' and resid 109 through 131 removed outlier: 3.689A pdb=" N VALI2 113 " --> pdb=" O SERI2 109 " (cutoff:3.500A) Processing helix chain 'I2' and resid 134 through 166 removed outlier: 3.502A pdb=" N LEUI2 138 " --> pdb=" O ILEI2 134 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHEI2 151 " --> pdb=" O GLYI2 147 " (cutoff:3.500A) Processing helix chain 'J2' and resid 97 through 107 Processing helix chain 'J2' and resid 110 through 131 removed outlier: 3.563A pdb=" N ALAJ2 114 " --> pdb=" O VALJ2 110 " (cutoff:3.500A) Processing helix chain 'J2' and resid 132 through 134 No H-bonds generated for 'chain 'J2' and resid 132 through 134' Processing helix chain 'J2' and resid 135 through 165 removed outlier: 3.797A pdb=" N THRJ2 140 " --> pdb=" O GLUJ2 136 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYRJ2 141 " --> pdb=" O ASPJ2 137 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHEJ2 151 " --> pdb=" O GLYJ2 147 " (cutoff:3.500A) Processing helix chain 'K2' and resid 97 through 107 removed outlier: 3.913A pdb=" N LEUK2 101 " --> pdb=" O GLYK2 97 " (cutoff:3.500A) Processing helix chain 'K2' and resid 108 through 131 removed outlier: 4.397A pdb=" N GLYK2 112 " --> pdb=" O METK2 108 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASNK2 131 " --> pdb=" O GLYK2 127 " (cutoff:3.500A) Processing helix chain 'K2' and resid 134 through 166 removed outlier: 3.637A pdb=" N LEUK2 138 " --> pdb=" O ILEK2 134 " (cutoff:3.500A) Processing helix chain 'M2' and resid 97 through 107 removed outlier: 3.537A pdb=" N LEUM2 101 " --> pdb=" O GLYM2 97 " (cutoff:3.500A) Processing helix chain 'M2' and resid 108 through 131 removed outlier: 4.497A pdb=" N GLYM2 112 " --> pdb=" O METM2 108 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALAM2 129 " --> pdb=" O VALM2 125 " (cutoff:3.500A) Processing helix chain 'M2' and resid 136 through 166 Processing helix chain 'N2' and resid 97 through 107 Processing helix chain 'N2' and resid 109 through 131 Processing helix chain 'N2' and resid 135 through 165 Processing helix chain 'O2' and resid 97 through 106 removed outlier: 4.162A pdb=" N LEUO2 101 " --> pdb=" O GLYO2 97 " (cutoff:3.500A) Processing helix chain 'O2' and resid 109 through 130 Processing helix chain 'O2' and resid 131 through 133 No H-bonds generated for 'chain 'O2' and resid 131 through 133' Processing helix chain 'O2' and resid 134 through 165 removed outlier: 3.691A pdb=" N THRO2 140 " --> pdb=" O GLUO2 136 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHEO2 148 " --> pdb=" O ILEO2 144 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHEO2 151 " --> pdb=" O GLYO2 147 " (cutoff:3.500A) Processing helix chain 'P2' and resid 98 through 107 Processing helix chain 'P2' and resid 108 through 131 removed outlier: 3.671A pdb=" N GLNP2 115 " --> pdb=" O GLYP2 111 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLYP2 116 " --> pdb=" O GLYP2 112 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SERP2 119 " --> pdb=" O GLNP2 115 " (cutoff:3.500A) Processing helix chain 'P2' and resid 138 through 165 Processing helix chain 'Q2' and resid 97 through 108 removed outlier: 4.020A pdb=" N ALAQ2 104 " --> pdb=" O SERQ2 100 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 109 through 129 removed outlier: 3.690A pdb=" N VALQ2 113 " --> pdb=" O SERQ2 109 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLNQ2 115 " --> pdb=" O GLYQ2 111 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLYQ2 116 " --> pdb=" O GLYQ2 112 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 130 through 133 removed outlier: 6.389A pdb=" N SERQ2 133 " --> pdb=" O ARGQ2 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q2' and resid 130 through 133' Processing helix chain 'Q2' and resid 134 through 166 removed outlier: 3.551A pdb=" N THRQ2 140 " --> pdb=" O GLUQ2 136 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHEQ2 151 " --> pdb=" O GLYQ2 147 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SERQ2 160 " --> pdb=" O CYSQ2 156 " (cutoff:3.500A) Processing helix chain 'L2' and resid 97 through 107 Processing helix chain 'L2' and resid 108 through 110 No H-bonds generated for 'chain 'L2' and resid 108 through 110' Processing helix chain 'L2' and resid 112 through 131 Processing helix chain 'L2' and resid 134 through 165 removed outlier: 3.510A pdb=" N PHEL2 148 " --> pdb=" O ILEL2 144 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILEL2 155 " --> pdb=" O PHEL2 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'g2' and resid 207 through 215 removed outlier: 6.863A pdb=" N ALAg2 207 " --> pdb=" O LYSg2 203 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYSg2 203 " --> pdb=" O ALAg2 207 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VALg2 215 " --> pdb=" O LEUg2 195 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEUg2 195 " --> pdb=" O VALg2 215 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASNg2 200 " --> pdb=" O LEUg2 110 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VALg2 107 " --> pdb=" O TYRg2 145 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VALg2 147 " --> pdb=" O VALg2 107 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALAg2 109 " --> pdb=" O VALg2 147 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VALg2 144 " --> pdb=" O LYSg2 164 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILEg2 166 " --> pdb=" O VALg2 144 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLYg2 146 " --> pdb=" O ILEg2 166 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THRg2 168 " --> pdb=" O GLYg2 146 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THRe2 52 " --> pdb=" O VALe2 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'g2' and resid 233 through 234 removed outlier: 5.826A pdb=" N GLUg2 233 " --> pdb=" O VALd2 84 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARGd2 86 " --> pdb=" O GLUg2 233 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLYd2 111 " --> pdb=" O LEUd2 87 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEUd2 46 " --> pdb=" O ALAd2 127 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VALd2 129 " --> pdb=" O LEUd2 46 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THRd2 48 " --> pdb=" O VALd2 129 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLYd2 131 " --> pdb=" O THRd2 48 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SERd2 50 " --> pdb=" O GLYd2 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'g2' and resid 233 through 234 removed outlier: 5.826A pdb=" N GLUg2 233 " --> pdb=" O VALd2 84 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ARGd2 86 " --> pdb=" O GLUg2 233 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLYd2 111 " --> pdb=" O LEUd2 87 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEUd2 46 " --> pdb=" O ALAd2 127 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VALd2 129 " --> pdb=" O LEUd2 46 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THRd2 48 " --> pdb=" O VALd2 129 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLYd2 131 " --> pdb=" O THRd2 48 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SERd2 50 " --> pdb=" O GLYd2 131 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLUd2 91 " --> pdb=" O PROd2 68 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 2169 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: 4.32 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9160 1.03 - 1.22: 19 1.22 - 1.42: 3656 1.42 - 1.61: 5270 1.61 - 1.81: 114 Bond restraints: 18219 Sorted by residual: bond pdb=" CB VALd2 113 " pdb=" CG1 VALd2 113 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.31e+00 bond pdb=" CB VALI2 125 " pdb=" CG2 VALI2 125 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.06e+00 bond pdb=" CG1 ILEI2 134 " pdb=" CD1 ILEI2 134 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.06e+00 bond pdb=" CG LEUL2 120 " pdb=" CD1 LEUL2 120 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 bond pdb=" CG LEUI2 120 " pdb=" CD2 LEUI2 120 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 ... (remaining 18214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 31006 1.20 - 2.40: 1835 2.40 - 3.59: 100 3.59 - 4.79: 17 4.79 - 5.99: 2 Bond angle restraints: 32960 Sorted by residual: angle pdb=" N LYSP2 135 " pdb=" CA LYSP2 135 " pdb=" C LYSP2 135 " ideal model delta sigma weight residual 112.04 108.43 3.61 1.44e+00 4.82e-01 6.30e+00 angle pdb=" C ILEI2 134 " pdb=" N LYSI2 135 " pdb=" CA LYSI2 135 " ideal model delta sigma weight residual 121.54 126.18 -4.64 1.91e+00 2.74e-01 5.91e+00 angle pdb=" C METP2 108 " pdb=" N SERP2 109 " pdb=" CA SERP2 109 " ideal model delta sigma weight residual 120.38 123.51 -3.13 1.46e+00 4.69e-01 4.61e+00 angle pdb=" C ILEg2 198 " pdb=" N TYRg2 199 " pdb=" CA TYRg2 199 " ideal model delta sigma weight residual 122.09 118.14 3.95 1.86e+00 2.89e-01 4.52e+00 angle pdb=" N LEUg2 245 " pdb=" CA LEUg2 245 " pdb=" C LEUg2 245 " ideal model delta sigma weight residual 112.23 109.60 2.63 1.26e+00 6.30e-01 4.36e+00 ... (remaining 32955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 7617 17.26 - 34.53: 642 34.53 - 51.79: 187 51.79 - 69.06: 91 69.06 - 86.32: 10 Dihedral angle restraints: 8547 sinusoidal: 4601 harmonic: 3946 Sorted by residual: dihedral pdb=" CA GLUg2 235 " pdb=" C GLUg2 235 " pdb=" N PROg2 236 " pdb=" CA PROg2 236 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ALAP2 114 " pdb=" C ALAP2 114 " pdb=" N GLNP2 115 " pdb=" CA GLNP2 115 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLNe2 47 " pdb=" C GLNe2 47 " pdb=" N GLYe2 48 " pdb=" CA GLYe2 48 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 833 0.030 - 0.060: 393 0.060 - 0.091: 174 0.091 - 0.121: 77 0.121 - 0.151: 9 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CG LEUd2 87 " pdb=" CB LEUd2 87 " pdb=" CD1 LEUd2 87 " pdb=" CD2 LEUd2 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CB VAL K 173 " pdb=" CA VAL K 173 " pdb=" CG1 VAL K 173 " pdb=" CG2 VAL K 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA PHEI2 121 " pdb=" N PHEI2 121 " pdb=" C PHEI2 121 " pdb=" CB PHEI2 121 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 1483 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHEO2 148 " -0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C PHEO2 148 " 0.076 2.00e-02 2.50e+03 pdb=" O PHEO2 148 " -0.028 2.00e-02 2.50e+03 pdb=" N LEUO2 149 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYI2 118 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C GLYI2 118 " -0.067 2.00e-02 2.50e+03 pdb=" O GLYI2 118 " 0.025 2.00e-02 2.50e+03 pdb=" N SERI2 119 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLYN2 118 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.46e+01 pdb=" C GLYN2 118 " 0.066 2.00e-02 2.50e+03 pdb=" O GLYN2 118 " -0.025 2.00e-02 2.50e+03 pdb=" N SERN2 119 " -0.022 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 796 2.17 - 2.78: 36999 2.78 - 3.39: 50843 3.39 - 3.99: 64269 3.99 - 4.60: 104944 Nonbonded interactions: 257851 Sorted by model distance: nonbonded pdb=" OG SERM2 100 " pdb=" HG SERL2 102 " model vdw 1.564 2.450 nonbonded pdb=" HG SERN2 109 " pdb=" O LEUO2 107 " model vdw 1.569 2.450 nonbonded pdb=" OE2 GLUg2 233 " pdb=" HG SERd2 81 " model vdw 1.572 2.450 nonbonded pdb=" O VALK2 157 " pdb=" HG SERK2 160 " model vdw 1.575 2.450 nonbonded pdb="HH21 ARG K 166 " pdb=" OE2 GLUP2 150 " model vdw 1.584 2.450 ... (remaining 257846 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 'H2' selection = chain 'I2' selection = chain 'J2' selection = chain 'K2' selection = chain 'L2' selection = chain 'M2' selection = chain 'N2' selection = chain 'O2' selection = chain 'P2' selection = chain 'Q2' } 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: 19.010 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: 0.110 Extract box with map and model: 0.330 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 20.040 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.007 0.056 9041 Z= 0.290 Angle : 0.616 5.989 12223 Z= 0.346 Chirality : 0.044 0.151 1486 Planarity : 0.007 0.044 1518 Dihedral : 13.813 86.321 3163 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.20), residues: 1174 helix: -2.43 (0.15), residues: 867 sheet: -3.57 (0.40), residues: 97 loop : -3.92 (0.30), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGN2 130 TYR 0.020 0.002 TYRg2 199 PHE 0.022 0.002 PHEg2 84 TRP 0.004 0.001 TRPe2 2 HIS 0.004 0.002 HISe2 39 Details of bonding type rmsd covalent geometry : bond 0.00738 ( 9041) covalent geometry : angle 0.61596 (12223) hydrogen bonds : bond 0.16010 ( 719) hydrogen bonds : angle 7.80582 ( 2169) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d2 54 GLU cc_start: 0.7914 (tt0) cc_final: 0.7585 (pm20) REVERT: e2 45 TYR cc_start: 0.8824 (m-80) cc_final: 0.8600 (m-80) REVERT: J2 137 ASP cc_start: 0.7880 (t70) cc_final: 0.7417 (t0) REVERT: M2 165 TYR cc_start: 0.6908 (m-10) cc_final: 0.6322 (m-80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2140 time to fit residues: 35.0714 Evaluate side-chains 96 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g2 179 GLN g2 261 ASN e2 36 ASN e2 57 ASN H2 115 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.143962 restraints weight = 26911.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.148466 restraints weight = 12250.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.151192 restraints weight = 6938.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152909 restraints weight = 4596.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153946 restraints weight = 3393.930| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9041 Z= 0.182 Angle : 0.560 5.127 12223 Z= 0.310 Chirality : 0.038 0.160 1486 Planarity : 0.005 0.045 1518 Dihedral : 4.444 23.508 1264 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.43 % Allowed : 10.63 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.24), residues: 1174 helix: -0.18 (0.17), residues: 904 sheet: -2.98 (0.43), residues: 96 loop : -2.31 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGd2 86 TYR 0.010 0.001 TYRg2 249 PHE 0.017 0.001 PHEI2 121 TRP 0.006 0.001 TRPe2 2 HIS 0.002 0.001 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9041) covalent geometry : angle 0.56037 (12223) hydrogen bonds : bond 0.05989 ( 719) hydrogen bonds : angle 4.95769 ( 2169) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.5592 (tpp) cc_final: 0.5272 (tpp) REVERT: g2 260 ASP cc_start: 0.8094 (m-30) cc_final: 0.7861 (m-30) REVERT: e2 53 ARG cc_start: 0.7133 (mtt90) cc_final: 0.6912 (ptp90) REVERT: J2 137 ASP cc_start: 0.7736 (t70) cc_final: 0.7143 (t0) REVERT: M2 165 TYR cc_start: 0.6850 (m-10) cc_final: 0.6347 (m-80) REVERT: N2 108 MET cc_start: 0.7355 (mtm) cc_final: 0.7085 (mtm) REVERT: Q2 146 MET cc_start: 0.7621 (mmm) cc_final: 0.7171 (mmm) outliers start: 4 outliers final: 4 residues processed: 113 average time/residue: 0.2163 time to fit residues: 33.8789 Evaluate side-chains 109 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g2 residue 153 SER Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.173351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155645 restraints weight = 27048.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.160413 restraints weight = 12458.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163310 restraints weight = 7168.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.165103 restraints weight = 4839.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.166162 restraints weight = 3659.792| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9041 Z= 0.195 Angle : 0.543 5.042 12223 Z= 0.299 Chirality : 0.038 0.141 1486 Planarity : 0.004 0.038 1518 Dihedral : 4.385 23.241 1264 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.17 % Allowed : 10.84 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1174 helix: 0.92 (0.18), residues: 903 sheet: -2.76 (0.47), residues: 92 loop : -1.57 (0.48), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGM2 130 TYR 0.009 0.001 TYRg2 249 PHE 0.014 0.001 PHEI2 121 TRP 0.007 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9041) covalent geometry : angle 0.54298 (12223) hydrogen bonds : bond 0.05834 ( 719) hydrogen bonds : angle 4.42791 ( 2169) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6150 (tpp) cc_final: 0.5940 (tpp) REVERT: d2 139 MET cc_start: 0.6428 (mmt) cc_final: 0.6143 (mmt) REVERT: H2 165 TYR cc_start: 0.5749 (m-10) cc_final: 0.5457 (m-10) REVERT: J2 137 ASP cc_start: 0.7791 (t70) cc_final: 0.7221 (t0) REVERT: J2 146 MET cc_start: 0.7977 (mmp) cc_final: 0.7674 (mmp) REVERT: M2 165 TYR cc_start: 0.6787 (m-10) cc_final: 0.6412 (m-80) REVERT: N2 146 MET cc_start: 0.7169 (mmm) cc_final: 0.6932 (mmm) outliers start: 11 outliers final: 7 residues processed: 136 average time/residue: 0.2459 time to fit residues: 45.0393 Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 153 SER Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g2 135 ASN e2 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.155584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137698 restraints weight = 28318.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142264 restraints weight = 13219.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.145101 restraints weight = 7750.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146917 restraints weight = 5252.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147915 restraints weight = 3947.092| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9041 Z= 0.187 Angle : 0.539 5.087 12223 Z= 0.295 Chirality : 0.037 0.150 1486 Planarity : 0.003 0.039 1518 Dihedral : 4.328 23.288 1264 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.28 % Allowed : 12.75 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.26), residues: 1174 helix: 1.25 (0.18), residues: 902 sheet: -2.35 (0.49), residues: 94 loop : -1.34 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGg2 157 TYR 0.007 0.001 TYRg2 199 PHE 0.014 0.001 PHEI2 121 TRP 0.005 0.001 TRPg2 175 HIS 0.003 0.001 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9041) covalent geometry : angle 0.53883 (12223) hydrogen bonds : bond 0.05563 ( 719) hydrogen bonds : angle 4.26335 ( 2169) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6493 (tpp) cc_final: 0.6144 (tpp) REVERT: g2 258 MET cc_start: 0.8028 (tpt) cc_final: 0.7526 (tpt) REVERT: J2 137 ASP cc_start: 0.7879 (t70) cc_final: 0.7478 (t0) REVERT: M2 165 TYR cc_start: 0.6758 (m-80) cc_final: 0.6489 (m-80) REVERT: O2 159 MET cc_start: 0.8003 (tpp) cc_final: 0.7740 (tpp) REVERT: P2 137 ASP cc_start: 0.7858 (t0) cc_final: 0.7305 (t0) REVERT: L2 150 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6918 (mt-10) outliers start: 12 outliers final: 9 residues processed: 137 average time/residue: 0.2334 time to fit residues: 44.0806 Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 153 SER Chi-restraints excluded: chain g2 residue 194 ARG Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain K2 residue 160 SER Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e2 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.152771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.135213 restraints weight = 28454.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139665 restraints weight = 13421.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142465 restraints weight = 7906.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144183 restraints weight = 5360.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145266 restraints weight = 4070.014| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9041 Z= 0.195 Angle : 0.537 5.211 12223 Z= 0.296 Chirality : 0.037 0.163 1486 Planarity : 0.004 0.040 1518 Dihedral : 4.313 24.218 1264 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.59 % Allowed : 12.96 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.26), residues: 1174 helix: 1.41 (0.18), residues: 901 sheet: -2.25 (0.47), residues: 94 loop : -1.23 (0.48), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGd2 63 TYR 0.007 0.001 TYRg2 199 PHE 0.013 0.001 PHEI2 121 TRP 0.005 0.001 TRPg2 175 HIS 0.001 0.000 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9041) covalent geometry : angle 0.53696 (12223) hydrogen bonds : bond 0.05617 ( 719) hydrogen bonds : angle 4.20234 ( 2169) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 157 MET cc_start: 0.6600 (tpp) cc_final: 0.6265 (tpp) REVERT: J2 137 ASP cc_start: 0.7863 (t70) cc_final: 0.7282 (t0) REVERT: M2 165 TYR cc_start: 0.6829 (m-80) cc_final: 0.6558 (m-80) REVERT: P2 137 ASP cc_start: 0.7819 (t0) cc_final: 0.7267 (t0) REVERT: L2 150 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6947 (mt-10) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 0.2373 time to fit residues: 41.8383 Evaluate side-chains 129 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 153 SER Chi-restraints excluded: chain g2 residue 194 ARG Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain K2 residue 160 SER Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 109 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.153339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135449 restraints weight = 28320.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.140027 restraints weight = 13398.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142824 restraints weight = 7831.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144604 restraints weight = 5328.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145720 restraints weight = 4011.291| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9041 Z= 0.175 Angle : 0.515 5.079 12223 Z= 0.283 Chirality : 0.037 0.148 1486 Planarity : 0.003 0.039 1518 Dihedral : 4.212 24.681 1264 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.34 % Allowed : 13.82 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.26), residues: 1174 helix: 1.58 (0.18), residues: 902 sheet: -2.16 (0.48), residues: 94 loop : -1.10 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGd2 63 TYR 0.006 0.001 TYRg2 249 PHE 0.013 0.001 PHEI2 121 TRP 0.004 0.001 TRPg2 175 HIS 0.001 0.000 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9041) covalent geometry : angle 0.51494 (12223) hydrogen bonds : bond 0.05408 ( 719) hydrogen bonds : angle 4.10462 ( 2169) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g2 258 MET cc_start: 0.8040 (tpt) cc_final: 0.7469 (tpt) REVERT: d2 151 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7177 (tm-30) REVERT: J2 137 ASP cc_start: 0.7882 (t70) cc_final: 0.7292 (t0) REVERT: O2 146 MET cc_start: 0.7936 (mmm) cc_final: 0.7673 (mmm) outliers start: 22 outliers final: 13 residues processed: 145 average time/residue: 0.2067 time to fit residues: 41.5858 Evaluate side-chains 137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 194 ARG Chi-restraints excluded: chain g2 residue 212 THR Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 76 MET Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain K2 residue 160 SER Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain P2 residue 155 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e2 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136206 restraints weight = 28438.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.140809 restraints weight = 13427.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143623 restraints weight = 7839.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145408 restraints weight = 5308.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.146503 restraints weight = 3999.163| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9041 Z= 0.162 Angle : 0.512 5.021 12223 Z= 0.279 Chirality : 0.036 0.139 1486 Planarity : 0.003 0.039 1518 Dihedral : 4.145 24.604 1264 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.59 % Allowed : 14.24 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.26), residues: 1174 helix: 1.69 (0.18), residues: 903 sheet: -2.07 (0.49), residues: 94 loop : -1.06 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGd2 63 TYR 0.006 0.001 TYRg2 249 PHE 0.012 0.001 PHEP2 121 TRP 0.004 0.001 TRPg2 175 HIS 0.001 0.000 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9041) covalent geometry : angle 0.51223 (12223) hydrogen bonds : bond 0.05279 ( 719) hydrogen bonds : angle 4.02239 ( 2169) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g2 258 MET cc_start: 0.8031 (tpt) cc_final: 0.7464 (tpt) REVERT: d2 151 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7219 (tm-30) REVERT: J2 137 ASP cc_start: 0.7873 (t70) cc_final: 0.7289 (t0) REVERT: Q2 146 MET cc_start: 0.7798 (mmm) cc_final: 0.6968 (tmm) outliers start: 15 outliers final: 14 residues processed: 138 average time/residue: 0.2202 time to fit residues: 42.5304 Evaluate side-chains 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 97 VAL Chi-restraints excluded: chain g2 residue 194 ARG Chi-restraints excluded: chain g2 residue 212 THR Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain L2 residue 154 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e2 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133131 restraints weight = 28781.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137475 restraints weight = 13846.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.140195 restraints weight = 8219.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.141938 restraints weight = 5627.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143011 restraints weight = 4248.117| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9041 Z= 0.200 Angle : 0.544 5.370 12223 Z= 0.300 Chirality : 0.037 0.142 1486 Planarity : 0.004 0.040 1518 Dihedral : 4.237 24.430 1264 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.44 % Allowed : 14.24 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.26), residues: 1174 helix: 1.63 (0.18), residues: 903 sheet: -2.15 (0.47), residues: 94 loop : -1.12 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGd2 63 TYR 0.008 0.001 TYRg2 199 PHE 0.014 0.001 PHEI2 121 TRP 0.005 0.001 TRPg2 175 HIS 0.002 0.000 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9041) covalent geometry : angle 0.54365 (12223) hydrogen bonds : bond 0.05571 ( 719) hydrogen bonds : angle 4.11795 ( 2169) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g2 258 MET cc_start: 0.8042 (tpt) cc_final: 0.7470 (tpt) REVERT: d2 151 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7270 (tm-30) REVERT: J2 137 ASP cc_start: 0.7940 (t70) cc_final: 0.7373 (t0) REVERT: O2 146 MET cc_start: 0.7998 (mmm) cc_final: 0.7680 (mmm) REVERT: Q2 146 MET cc_start: 0.7890 (mmm) cc_final: 0.7011 (tmm) outliers start: 23 outliers final: 13 residues processed: 151 average time/residue: 0.2129 time to fit residues: 44.8328 Evaluate side-chains 141 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 97 VAL Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain e2 residue 3 ARG Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain K2 residue 160 SER Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain L2 residue 154 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.151162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133375 restraints weight = 28657.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.137915 restraints weight = 13627.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140712 restraints weight = 7989.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.142482 restraints weight = 5426.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143676 restraints weight = 4080.490| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9041 Z= 0.194 Angle : 0.542 5.301 12223 Z= 0.298 Chirality : 0.037 0.150 1486 Planarity : 0.003 0.040 1518 Dihedral : 4.234 24.216 1264 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.81 % Allowed : 15.41 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.26), residues: 1174 helix: 1.65 (0.18), residues: 903 sheet: -2.17 (0.48), residues: 94 loop : -1.14 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGd2 63 TYR 0.007 0.001 TYRg2 249 PHE 0.012 0.001 PHEI2 121 TRP 0.004 0.001 TRPg2 175 HIS 0.002 0.001 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 9041) covalent geometry : angle 0.54155 (12223) hydrogen bonds : bond 0.05533 ( 719) hydrogen bonds : angle 4.11309 ( 2169) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g2 258 MET cc_start: 0.8033 (tpt) cc_final: 0.7460 (tpt) REVERT: d2 151 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7242 (tm-30) REVERT: J2 137 ASP cc_start: 0.7933 (t70) cc_final: 0.7370 (t0) REVERT: N2 158 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8059 (mm) REVERT: P2 137 ASP cc_start: 0.7952 (t0) cc_final: 0.7182 (t0) REVERT: Q2 146 MET cc_start: 0.7864 (mmm) cc_final: 0.6883 (tmm) outliers start: 17 outliers final: 16 residues processed: 145 average time/residue: 0.2022 time to fit residues: 41.6951 Evaluate side-chains 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 97 VAL Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 76 MET Chi-restraints excluded: chain e2 residue 3 ARG Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain K2 residue 160 SER Chi-restraints excluded: chain M2 residue 137 ASP Chi-restraints excluded: chain N2 residue 158 LEU Chi-restraints excluded: chain O2 residue 120 LEU Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain L2 residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.159048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140210 restraints weight = 30008.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144843 restraints weight = 14970.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.147686 restraints weight = 9020.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149652 restraints weight = 6227.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.150851 restraints weight = 4706.486| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9041 Z= 0.157 Angle : 0.519 5.072 12223 Z= 0.282 Chirality : 0.037 0.147 1486 Planarity : 0.003 0.040 1518 Dihedral : 4.127 24.405 1264 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.81 % Allowed : 15.83 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1174 helix: 1.79 (0.18), residues: 910 sheet: -2.13 (0.48), residues: 94 loop : -1.19 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGd2 63 TYR 0.006 0.001 TYRg2 249 PHE 0.011 0.001 PHEI2 121 TRP 0.003 0.001 TRPg2 175 HIS 0.001 0.001 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9041) covalent geometry : angle 0.51909 (12223) hydrogen bonds : bond 0.05238 ( 719) hydrogen bonds : angle 4.00999 ( 2169) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: g2 258 MET cc_start: 0.8004 (tpt) cc_final: 0.7468 (tpt) REVERT: d2 151 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7273 (tm-30) REVERT: J2 137 ASP cc_start: 0.7917 (t70) cc_final: 0.7488 (t0) REVERT: N2 158 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8044 (mm) REVERT: O2 146 MET cc_start: 0.7968 (mmm) cc_final: 0.7708 (mmm) REVERT: P2 137 ASP cc_start: 0.7967 (t0) cc_final: 0.7222 (t0) REVERT: Q2 146 MET cc_start: 0.7827 (mmm) cc_final: 0.6879 (tmm) outliers start: 17 outliers final: 14 residues processed: 141 average time/residue: 0.2097 time to fit residues: 41.9346 Evaluate side-chains 142 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain g2 residue 97 VAL Chi-restraints excluded: chain g2 residue 253 THR Chi-restraints excluded: chain d2 residue 44 GLN Chi-restraints excluded: chain d2 residue 48 THR Chi-restraints excluded: chain d2 residue 50 SER Chi-restraints excluded: chain d2 residue 76 MET Chi-restraints excluded: chain e2 residue 3 ARG Chi-restraints excluded: chain H2 residue 155 ILE Chi-restraints excluded: chain I2 residue 155 ILE Chi-restraints excluded: chain K2 residue 156 CYS Chi-restraints excluded: chain K2 residue 160 SER Chi-restraints excluded: chain N2 residue 158 LEU Chi-restraints excluded: chain P2 residue 155 ILE Chi-restraints excluded: chain L2 residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.158880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140326 restraints weight = 30051.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.144837 restraints weight = 14772.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147694 restraints weight = 8949.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149570 restraints weight = 6171.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150824 restraints weight = 4675.909| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9041 Z= 0.165 Angle : 0.522 6.083 12223 Z= 0.285 Chirality : 0.037 0.138 1486 Planarity : 0.003 0.040 1518 Dihedral : 4.105 24.075 1264 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.70 % Allowed : 16.37 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.26), residues: 1174 helix: 1.82 (0.18), residues: 910 sheet: -2.17 (0.48), residues: 94 loop : -1.20 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGd2 63 TYR 0.006 0.001 TYRg2 249 PHE 0.013 0.001 PHEO2 148 TRP 0.004 0.001 TRPg2 175 HIS 0.001 0.001 HISd2 80 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9041) covalent geometry : angle 0.52228 (12223) hydrogen bonds : bond 0.05261 ( 719) hydrogen bonds : angle 4.01027 ( 2169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3013.51 seconds wall clock time: 52 minutes 9.32 seconds (3129.32 seconds total)