Starting phenix.real_space_refine on Thu Jul 31 07:33:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5l08_8300/07_2025/5l08_8300.cif Found real_map, /net/cci-nas-00/data/ceres_data/5l08_8300/07_2025/5l08_8300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5l08_8300/07_2025/5l08_8300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5l08_8300/07_2025/5l08_8300.map" model { file = "/net/cci-nas-00/data/ceres_data/5l08_8300/07_2025/5l08_8300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5l08_8300/07_2025/5l08_8300.cif" } resolution = 4.6 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 ------------------------------------------------------------------------------- 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= -31.220 sd= 18.086 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 72 5.16 5 C 8658 2.51 5 N 2286 2.21 5 O 2601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13617 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "C" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "D" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "E" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "F" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "G" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "H" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Chain: "I" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 3, 'TRANS': 177} Time building chain proxies: 7.96, per 1000 atoms: 0.58 Number of scatterers: 13617 At special positions: 0 Unit cell: (102.92, 103.54, 125.24, 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 72 16.00 O 2601 8.00 N 2286 7.00 C 8658 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: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3186 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 0 sheets defined 75.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 8 through 13 removed outlier: 3.655A pdb=" N GLY A 11 " --> pdb=" O TYR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 82 through 91 removed outlier: 3.619A pdb=" N ARG A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 3.603A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 168 removed outlier: 4.294A pdb=" N VAL A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.990A pdb=" N LYS A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'B' and resid 2 through 2 No H-bonds generated for 'chain 'B' and resid 2 through 2' Processing helix chain 'B' and resid 3 through 12 removed outlier: 3.807A pdb=" N ASP B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.535A pdb=" N ILE B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 113 through 128 removed outlier: 4.761A pdb=" N GLU B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'C' and resid 3 through 6 Processing helix chain 'C' and resid 7 through 12 removed outlier: 3.874A pdb=" N GLY C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 12 " --> pdb=" O TYR C 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 12' Processing helix chain 'C' and resid 15 through 27 Processing helix chain 'C' and resid 40 through 51 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 83 through 91 removed outlier: 4.117A pdb=" N GLU C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.972A pdb=" N SER C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 156 through 165 removed outlier: 3.685A pdb=" N LYS C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 8 through 14 removed outlier: 4.576A pdb=" N GLY D 11 " --> pdb=" O TYR D 8 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU D 12 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 27 through 29 No H-bonds generated for 'chain 'D' and resid 27 through 29' Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 71 through 78 removed outlier: 3.520A pdb=" N LEU D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 113 through 128 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 156 through 166 removed outlier: 3.525A pdb=" N LEU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.719A pdb=" N LEU D 172 " --> pdb=" O ASN D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'E' and resid 2 through 2 No H-bonds generated for 'chain 'E' and resid 2 through 2' Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.844A pdb=" N ASP E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 40 through 51 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 71 through 78 Processing helix chain 'E' and resid 83 through 90 Processing helix chain 'E' and resid 99 through 112 Processing helix chain 'E' and resid 113 through 128 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 156 through 166 removed outlier: 3.605A pdb=" N LEU E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 removed outlier: 3.796A pdb=" N LEU E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'F' and resid 2 through 2 No H-bonds generated for 'chain 'F' and resid 2 through 2' Processing helix chain 'F' and resid 3 through 12 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 40 through 51 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 71 through 76 Processing helix chain 'F' and resid 82 through 88 removed outlier: 3.576A pdb=" N MET F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 92 removed outlier: 3.655A pdb=" N THR F 92 " --> pdb=" O GLU F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 92' Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 113 through 128 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 156 through 166 removed outlier: 4.166A pdb=" N LEU F 160 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 170 removed outlier: 6.968A pdb=" N SER F 170 " --> pdb=" O ILE F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 167 through 170' Processing helix chain 'F' and resid 171 through 176 Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'G' and resid 2 through 2 No H-bonds generated for 'chain 'G' and resid 2 through 2' Processing helix chain 'G' and resid 3 through 8 Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 27 through 29 No H-bonds generated for 'chain 'G' and resid 27 through 29' Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 40 through 51 removed outlier: 4.120A pdb=" N LYS G 51 " --> pdb=" O ARG G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 71 through 78 removed outlier: 3.579A pdb=" N LEU G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 90 removed outlier: 4.338A pdb=" N MET G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 112 Processing helix chain 'G' and resid 113 through 128 removed outlier: 3.518A pdb=" N SER G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 148 Processing helix chain 'G' and resid 153 through 157 Processing helix chain 'G' and resid 158 through 159 No H-bonds generated for 'chain 'G' and resid 158 through 159' Processing helix chain 'G' and resid 160 through 165 Processing helix chain 'G' and resid 168 through 176 removed outlier: 3.677A pdb=" N LEU G 172 " --> pdb=" O ASN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 182 removed outlier: 4.692A pdb=" N GLU G 180 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 14 removed outlier: 3.861A pdb=" N TYR H 8 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP H 9 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 26 removed outlier: 4.064A pdb=" N ALA H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 29 No H-bonds generated for 'chain 'H' and resid 27 through 29' Processing helix chain 'H' and resid 31 through 36 Processing helix chain 'H' and resid 40 through 51 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 71 through 78 removed outlier: 3.544A pdb=" N LEU H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 91 removed outlier: 3.675A pdb=" N GLU H 89 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 112 Processing helix chain 'H' and resid 113 through 128 Processing helix chain 'H' and resid 138 through 149 Processing helix chain 'H' and resid 156 through 159 Processing helix chain 'H' and resid 160 through 165 Processing helix chain 'H' and resid 168 through 176 removed outlier: 3.609A pdb=" N LEU H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 182 Processing helix chain 'I' and resid 2 through 8 removed outlier: 3.537A pdb=" N TYR I 8 " --> pdb=" O ARG I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 14 removed outlier: 4.169A pdb=" N GLN I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 26 Processing helix chain 'I' and resid 27 through 29 No H-bonds generated for 'chain 'I' and resid 27 through 29' Processing helix chain 'I' and resid 31 through 36 Processing helix chain 'I' and resid 40 through 51 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 71 through 77 removed outlier: 3.975A pdb=" N ILE I 76 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 91 Processing helix chain 'I' and resid 99 through 112 Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 138 through 149 Processing helix chain 'I' and resid 156 through 159 Processing helix chain 'I' and resid 160 through 165 Processing helix chain 'I' and resid 168 through 176 removed outlier: 3.613A pdb=" N LEU I 172 " --> pdb=" O ASN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 182 668 hydrogen bonds defined for protein. 1806 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: 3.69 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2473 1.31 - 1.44: 3098 1.44 - 1.56: 8073 1.56 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 13770 Sorted by residual: bond pdb=" C TYR E 8 " pdb=" O TYR E 8 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.15e-02 7.56e+03 1.67e+01 bond pdb=" C TYR B 8 " pdb=" O TYR B 8 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.15e-02 7.56e+03 1.67e+01 bond pdb=" C TYR H 8 " pdb=" O TYR H 8 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.15e-02 7.56e+03 1.66e+01 bond pdb=" C TYR F 8 " pdb=" O TYR F 8 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.61e+01 bond pdb=" C TYR C 8 " pdb=" O TYR C 8 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.15e-02 7.56e+03 1.58e+01 ... (remaining 13765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 17746 2.32 - 4.63: 597 4.63 - 6.95: 63 6.95 - 9.26: 4 9.26 - 11.58: 4 Bond angle restraints: 18414 Sorted by residual: angle pdb=" C GLU F 36 " pdb=" N PRO F 37 " pdb=" CA PRO F 37 " ideal model delta sigma weight residual 120.83 114.92 5.91 1.02e+00 9.61e-01 3.35e+01 angle pdb=" O LEU H 7 " pdb=" C LEU H 7 " pdb=" N TYR H 8 " ideal model delta sigma weight residual 122.12 127.51 -5.39 1.06e+00 8.90e-01 2.59e+01 angle pdb=" O LEU E 7 " pdb=" C LEU E 7 " pdb=" N TYR E 8 " ideal model delta sigma weight residual 122.12 127.46 -5.34 1.06e+00 8.90e-01 2.54e+01 angle pdb=" O LEU F 7 " pdb=" C LEU F 7 " pdb=" N TYR F 8 " ideal model delta sigma weight residual 122.12 127.45 -5.33 1.06e+00 8.90e-01 2.53e+01 angle pdb=" O LEU B 7 " pdb=" C LEU B 7 " pdb=" N TYR B 8 " ideal model delta sigma weight residual 122.12 127.43 -5.31 1.06e+00 8.90e-01 2.51e+01 ... (remaining 18409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8342 17.69 - 35.37: 253 35.37 - 53.06: 95 53.06 - 70.75: 39 70.75 - 88.44: 10 Dihedral angle restraints: 8739 sinusoidal: 3879 harmonic: 4860 Sorted by residual: dihedral pdb=" CB GLU F 55 " pdb=" CG GLU F 55 " pdb=" CD GLU F 55 " pdb=" OE1 GLU F 55 " ideal model delta sinusoidal sigma weight residual 0.00 88.44 -88.44 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA ASP C 15 " pdb=" CB ASP C 15 " pdb=" CG ASP C 15 " pdb=" OD1 ASP C 15 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CB GLU A 89 " pdb=" CG GLU A 89 " pdb=" CD GLU A 89 " pdb=" OE1 GLU A 89 " ideal model delta sinusoidal sigma weight residual 0.00 86.06 -86.06 1 3.00e+01 1.11e-03 9.93e+00 ... (remaining 8736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1200 0.028 - 0.055: 343 0.055 - 0.083: 86 0.083 - 0.110: 352 0.110 - 0.138: 89 Chirality restraints: 2070 Sorted by residual: chirality pdb=" CA VAL C 150 " pdb=" N VAL C 150 " pdb=" C VAL C 150 " pdb=" CB VAL C 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL H 150 " pdb=" N VAL H 150 " pdb=" C VAL H 150 " pdb=" CB VAL H 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL E 150 " pdb=" N VAL E 150 " pdb=" C VAL E 150 " pdb=" CB VAL E 150 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2067 not shown) Planarity restraints: 2367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 32 " 0.014 2.00e-02 2.50e+03 3.00e-02 9.02e+00 pdb=" C GLN F 32 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN F 32 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG F 33 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 32 " 0.014 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C GLN A 32 " -0.052 2.00e-02 2.50e+03 pdb=" O GLN A 32 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 33 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 32 " -0.014 2.00e-02 2.50e+03 2.99e-02 8.91e+00 pdb=" C GLN B 32 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN B 32 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG B 33 " -0.018 2.00e-02 2.50e+03 ... (remaining 2364 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 102 2.61 - 3.18: 13739 3.18 - 3.76: 20829 3.76 - 4.33: 32333 4.33 - 4.90: 48222 Nonbonded interactions: 115225 Sorted by model distance: nonbonded pdb=" CE1 PHE A 122 " pdb=" O LEU B 42 " model vdw 2.041 3.340 nonbonded pdb=" O GLU F 127 " pdb=" CG1 ILE F 128 " model vdw 2.236 3.440 nonbonded pdb=" O ARG F 118 " pdb=" CD2 PHE F 122 " model vdw 2.239 3.340 nonbonded pdb=" O GLU C 127 " pdb=" CG1 ILE C 128 " model vdw 2.257 3.440 nonbonded pdb=" O GLU A 127 " pdb=" CG1 ILE A 128 " model vdw 2.259 3.440 ... (remaining 115220 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set refine NCS operators NCS operators will be refined. 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 31.520 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 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 : 0.011 0.053 13770 Z= 0.631 Angle : 1.031 11.579 18414 Z= 0.757 Chirality : 0.051 0.138 2070 Planarity : 0.003 0.030 2367 Dihedral : 11.660 88.436 5553 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.04 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: -0.41 (0.22), residues: 1611 helix: -1.38 (0.15), residues: 952 sheet: None (None), residues: 0 loop : 1.97 (0.29), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE F 45 TYR 0.007 0.000 TYR D 29 ARG 0.003 0.000 ARG A 71 Details of bonding type rmsd hydrogen bonds : bond 0.19228 ( 668) hydrogen bonds : angle 7.26414 ( 1806) covalent geometry : bond 0.01100 (13770) covalent geometry : angle 1.03062 (18414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3222 Ramachandran restraints generated. 1611 Oldfield, 0 Emsley, 1611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LEU cc_start: 0.7137 (mt) cc_final: 0.6885 (mt) REVERT: A 40 ASP cc_start: 0.8831 (p0) cc_final: 0.8541 (p0) REVERT: A 51 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8632 (mmtm) REVERT: A 61 PHE cc_start: 0.8366 (t80) cc_final: 0.7560 (t80) REVERT: A 62 LEU cc_start: 0.9136 (tp) cc_final: 0.8875 (tp) REVERT: A 69 ILE cc_start: 0.9271 (pt) cc_final: 0.9019 (mp) REVERT: A 74 LEU cc_start: 0.9180 (mt) cc_final: 0.8972 (mt) REVERT: A 97 GLN cc_start: 0.7430 (mm-40) cc_final: 0.7018 (mt0) REVERT: A 103 VAL cc_start: 0.8960 (p) cc_final: 0.8383 (m) REVERT: A 106 TYR cc_start: 0.8451 (t80) cc_final: 0.8054 (t80) REVERT: A 151 ILE cc_start: 0.8064 (pt) cc_final: 0.7769 (pt) REVERT: A 152 LEU cc_start: 0.7996 (tp) cc_final: 0.7624 (tp) REVERT: A 160 LEU cc_start: 0.8948 (mt) cc_final: 0.8563 (mt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2113 time to fit residues: 24.2388 Evaluate side-chains 68 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0570 chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.0050 chunk 82 optimal weight: 0.2980 chunk 65 optimal weight: 0.1980 chunk 126 optimal weight: 30.0000 chunk 49 optimal weight: 0.0770 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 147 optimal weight: 0.0980 overall best weight: 0.0870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.121369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106118 restraints weight = 5114.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108941 restraints weight = 3237.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.111135 restraints weight = 2309.213| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 1.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 13770 Z= 0.307 Angle : 1.251 17.021 18414 Z= 0.650 Chirality : 0.058 0.249 2070 Planarity : 0.016 0.207 2367 Dihedral : 7.201 25.249 1800 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 32.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.16 % Allowed : 5.81 % Favored : 93.02 % 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: -2.15 (0.19), residues: 1611 helix: -1.87 (0.12), residues: 1188 sheet: None (None), residues: 0 loop : 0.78 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE A 120 TYR 0.016 0.002 TYR F 8 ARG 0.021 0.001 ARG B 33 Details of bonding type rmsd hydrogen bonds : bond 0.13550 ( 668) hydrogen bonds : angle 8.74295 ( 1806) covalent geometry : bond 0.00674 (13770) covalent geometry : angle 1.25059 (18414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.8337 (m-30) cc_final: 0.7940 (p0) REVERT: F 5 ARG cc_start: 0.8538 (mtt180) cc_final: 0.7915 (tpp-160) REVERT: F 24 PHE cc_start: 0.8578 (t80) cc_final: 0.8271 (t80) REVERT: F 44 LEU cc_start: 0.9777 (tp) cc_final: 0.9561 (tp) REVERT: F 48 LEU cc_start: 0.9550 (mt) cc_final: 0.9181 (mt) REVERT: F 54 LEU cc_start: 0.8556 (tt) cc_final: 0.8308 (tt) REVERT: F 64 GLU cc_start: 0.8371 (pt0) cc_final: 0.7907 (pt0) REVERT: F 65 LEU cc_start: 0.9153 (mm) cc_final: 0.8674 (mm) REVERT: F 67 PHE cc_start: 0.8643 (t80) cc_final: 0.7979 (t80) REVERT: F 68 ARG cc_start: 0.8921 (mmm160) cc_final: 0.7878 (mmm160) REVERT: F 86 MET cc_start: 0.7426 (mmp) cc_final: 0.6659 (mmt) REVERT: F 107 GLN cc_start: 0.8697 (mp10) cc_final: 0.8410 (mp10) REVERT: F 133 LEU cc_start: 0.6712 (mt) cc_final: 0.6460 (mt) REVERT: F 137 MET cc_start: 0.7432 (mtt) cc_final: 0.6952 (mtt) REVERT: F 143 PHE cc_start: 0.9280 (m-10) cc_final: 0.8949 (m-10) REVERT: F 152 LEU cc_start: 0.7556 (tp) cc_final: 0.6984 (tp) REVERT: F 168 ASN cc_start: 0.5760 (t0) cc_final: 0.4880 (t0) REVERT: F 173 LYS cc_start: 0.8842 (ptmm) cc_final: 0.8022 (mptt) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.1930 time to fit residues: 23.9135 Evaluate side-chains 81 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 0.9980 chunk 14 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 36 optimal weight: 40.0000 chunk 156 optimal weight: 1.9990 chunk 159 optimal weight: 0.0870 chunk 93 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 15 optimal weight: 0.1980 chunk 32 optimal weight: 20.0000 overall best weight: 1.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.114113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097794 restraints weight = 5265.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100237 restraints weight = 3680.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.102109 restraints weight = 2796.976| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 1.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 13770 Z= 0.257 Angle : 1.258 14.989 18414 Z= 0.645 Chirality : 0.057 0.193 2070 Planarity : 0.010 0.134 2367 Dihedral : 7.463 25.302 1800 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 39.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % 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: -2.43 (0.19), residues: 1611 helix: -1.95 (0.13), residues: 1134 sheet: None (None), residues: 0 loop : -0.09 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.003 PHE D 122 TYR 0.012 0.003 TYR C 8 ARG 0.006 0.001 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.11236 ( 668) hydrogen bonds : angle 8.36514 ( 1806) covalent geometry : bond 0.00578 (13770) covalent geometry : angle 1.25753 (18414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.7994 (m-30) cc_final: 0.7589 (m-30) REVERT: F 44 LEU cc_start: 0.9779 (tp) cc_final: 0.9525 (tp) REVERT: F 48 LEU cc_start: 0.9505 (mt) cc_final: 0.9263 (mt) REVERT: F 53 MET cc_start: 0.8026 (mpp) cc_final: 0.7758 (mtm) REVERT: F 61 PHE cc_start: 0.8280 (t80) cc_final: 0.7473 (t80) REVERT: F 97 GLN cc_start: 0.8697 (tt0) cc_final: 0.8184 (tp40) REVERT: F 142 ILE cc_start: 0.8135 (mm) cc_final: 0.7717 (mm) REVERT: F 143 PHE cc_start: 0.9314 (m-10) cc_final: 0.9063 (m-10) REVERT: F 162 ARG cc_start: 0.7828 (tpt90) cc_final: 0.7593 (tpt170) REVERT: F 168 ASN cc_start: 0.6753 (t0) cc_final: 0.5426 (t0) REVERT: F 173 LYS cc_start: 0.8845 (ptmm) cc_final: 0.8399 (mptt) REVERT: F 178 TYR cc_start: 0.8544 (t80) cc_final: 0.8116 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1880 time to fit residues: 20.8231 Evaluate side-chains 80 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 76 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 143 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 131 optimal weight: 0.0370 chunk 123 optimal weight: 0.7980 overall best weight: 3.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 49 GLN F 70 ASN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.113184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095639 restraints weight = 5195.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.098065 restraints weight = 3504.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.099896 restraints weight = 2595.688| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 1.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 13770 Z= 0.308 Angle : 1.319 14.735 18414 Z= 0.689 Chirality : 0.058 0.209 2070 Planarity : 0.011 0.108 2367 Dihedral : 7.824 28.242 1800 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 46.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.89 (0.21), residues: 1611 helix: -1.82 (0.14), residues: 1098 sheet: None (None), residues: 0 loop : 0.67 (0.33), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.063 0.004 PHE D 122 TYR 0.039 0.003 TYR I 8 ARG 0.026 0.003 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.11027 ( 668) hydrogen bonds : angle 8.55040 ( 1806) covalent geometry : bond 0.00716 (13770) covalent geometry : angle 1.31889 (18414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.6879 (m-30) cc_final: 0.5899 (m-30) REVERT: F 53 MET cc_start: 0.7991 (mpp) cc_final: 0.7771 (mtm) REVERT: F 54 LEU cc_start: 0.9088 (tt) cc_final: 0.8111 (tt) REVERT: F 55 GLU cc_start: 0.7878 (pm20) cc_final: 0.7200 (pm20) REVERT: F 59 LEU cc_start: 0.7593 (mt) cc_final: 0.7388 (mt) REVERT: F 74 LEU cc_start: 0.9271 (mt) cc_final: 0.8543 (mt) REVERT: F 79 LEU cc_start: 0.8083 (mm) cc_final: 0.7306 (tt) REVERT: F 104 MET cc_start: 0.8691 (ptt) cc_final: 0.8291 (ppp) REVERT: F 122 PHE cc_start: 0.7440 (t80) cc_final: 0.7145 (t80) REVERT: F 142 ILE cc_start: 0.8153 (mm) cc_final: 0.7579 (mm) REVERT: F 143 PHE cc_start: 0.9133 (m-10) cc_final: 0.8823 (m-10) REVERT: F 161 LYS cc_start: 0.7630 (mtmt) cc_final: 0.7408 (mtmm) REVERT: F 168 ASN cc_start: 0.7109 (t0) cc_final: 0.5879 (t0) REVERT: F 173 LYS cc_start: 0.8944 (ptmm) cc_final: 0.8475 (mptt) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1610 time to fit residues: 16.9723 Evaluate side-chains 79 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 104 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 0.0070 chunk 107 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 124 optimal weight: 0.0670 chunk 111 optimal weight: 5.9990 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.119463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102181 restraints weight = 4889.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104717 restraints weight = 3367.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106634 restraints weight = 2535.322| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 1.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13770 Z= 0.253 Angle : 1.264 17.353 18414 Z= 0.655 Chirality : 0.060 0.271 2070 Planarity : 0.007 0.065 2367 Dihedral : 7.524 28.554 1800 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 37.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.46 (0.19), residues: 1611 helix: -1.91 (0.13), residues: 1080 sheet: None (None), residues: 0 loop : -0.51 (0.30), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.004 PHE A 122 TYR 0.066 0.005 TYR F 8 ARG 0.010 0.002 ARG B 71 Details of bonding type rmsd hydrogen bonds : bond 0.10630 ( 668) hydrogen bonds : angle 8.03611 ( 1806) covalent geometry : bond 0.00540 (13770) covalent geometry : angle 1.26365 (18414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 ASP cc_start: 0.6558 (m-30) cc_final: 0.6350 (m-30) REVERT: D 47 ARG cc_start: 0.9041 (mmp80) cc_final: 0.8829 (mmp80) REVERT: D 48 LEU cc_start: 0.9648 (mt) cc_final: 0.9270 (mt) REVERT: D 52 ARG cc_start: 0.7768 (mpt90) cc_final: 0.7373 (mtm-85) REVERT: D 53 MET cc_start: 0.8035 (mpp) cc_final: 0.7785 (mpp) REVERT: D 68 ARG cc_start: 0.8424 (mmt-90) cc_final: 0.8142 (mpt180) REVERT: D 70 ASN cc_start: 0.8099 (m110) cc_final: 0.7809 (m110) REVERT: D 72 LEU cc_start: 0.7867 (pt) cc_final: 0.6807 (mt) REVERT: D 85 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7589 (tp30) REVERT: D 97 GLN cc_start: 0.7052 (tp40) cc_final: 0.6325 (tp40) REVERT: D 101 TYR cc_start: 0.7379 (t80) cc_final: 0.6869 (t80) REVERT: D 118 ARG cc_start: 0.8493 (ttt-90) cc_final: 0.8108 (ttm110) REVERT: D 142 ILE cc_start: 0.8370 (mm) cc_final: 0.7606 (mm) REVERT: D 143 PHE cc_start: 0.8955 (m-10) cc_final: 0.8486 (m-10) REVERT: D 152 LEU cc_start: 0.8098 (tp) cc_final: 0.7817 (tp) REVERT: D 168 ASN cc_start: 0.6288 (t0) cc_final: 0.5087 (t0) REVERT: D 178 TYR cc_start: 0.8158 (t80) cc_final: 0.7816 (t80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2021 time to fit residues: 21.9829 Evaluate side-chains 79 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 0.1980 chunk 130 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 73 optimal weight: 0.0370 chunk 21 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 152 optimal weight: 8.9990 chunk 149 optimal weight: 40.0000 overall best weight: 3.6464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 ASN D 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.119201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104226 restraints weight = 5439.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.106790 restraints weight = 3657.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108720 restraints weight = 2688.062| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 1.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13770 Z= 0.245 Angle : 1.233 16.439 18414 Z= 0.663 Chirality : 0.054 0.200 2070 Planarity : 0.013 0.148 2367 Dihedral : 7.670 27.749 1800 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 36.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -2.93 (0.19), residues: 1611 helix: -2.37 (0.12), residues: 1143 sheet: None (None), residues: 0 loop : -0.08 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.065 0.004 PHE I 122 TYR 0.101 0.007 TYR G 8 ARG 0.010 0.002 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.10076 ( 668) hydrogen bonds : angle 8.05504 ( 1806) covalent geometry : bond 0.00526 (13770) covalent geometry : angle 1.23269 (18414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.9637 (mt) cc_final: 0.9326 (mt) REVERT: D 49 GLN cc_start: 0.9101 (tp40) cc_final: 0.8462 (mm110) REVERT: D 53 MET cc_start: 0.8220 (mpp) cc_final: 0.7882 (mpp) REVERT: D 61 PHE cc_start: 0.8829 (t80) cc_final: 0.8053 (t80) REVERT: D 76 ILE cc_start: 0.8508 (mp) cc_final: 0.8252 (mm) REVERT: D 86 MET cc_start: 0.7991 (mmm) cc_final: 0.7695 (mmm) REVERT: D 101 TYR cc_start: 0.7681 (t80) cc_final: 0.7358 (t80) REVERT: D 104 MET cc_start: 0.9022 (ptt) cc_final: 0.8471 (ppp) REVERT: D 105 LEU cc_start: 0.9257 (mt) cc_final: 0.8961 (mt) REVERT: D 118 ARG cc_start: 0.8405 (ttt-90) cc_final: 0.8078 (ttm110) REVERT: D 142 ILE cc_start: 0.8317 (mm) cc_final: 0.7642 (mm) REVERT: D 143 PHE cc_start: 0.8926 (m-10) cc_final: 0.8397 (m-10) REVERT: D 152 LEU cc_start: 0.8115 (tp) cc_final: 0.7769 (tp) REVERT: D 154 GLU cc_start: 0.7434 (mp0) cc_final: 0.6831 (mm-30) REVERT: D 168 ASN cc_start: 0.6141 (t0) cc_final: 0.5120 (t0) REVERT: D 169 LYS cc_start: 0.7781 (pttm) cc_final: 0.7504 (pttp) REVERT: D 173 LYS cc_start: 0.9095 (ptmm) cc_final: 0.8806 (mptt) REVERT: D 178 TYR cc_start: 0.8193 (t80) cc_final: 0.6855 (t80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2022 time to fit residues: 19.6396 Evaluate side-chains 75 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 40.0000 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 40.0000 chunk 98 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 40.0000 chunk 134 optimal weight: 7.9990 chunk 72 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.121615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105416 restraints weight = 5100.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107965 restraints weight = 3510.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.109700 restraints weight = 2618.602| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 1.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13770 Z= 0.215 Angle : 1.238 14.087 18414 Z= 0.637 Chirality : 0.056 0.295 2070 Planarity : 0.008 0.054 2367 Dihedral : 7.475 26.222 1800 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 39.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.03 (0.18), residues: 1611 helix: -2.32 (0.12), residues: 1125 sheet: None (None), residues: 0 loop : -0.61 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.003 PHE B 122 TYR 0.088 0.007 TYR B 8 ARG 0.013 0.001 ARG G 33 Details of bonding type rmsd hydrogen bonds : bond 0.10217 ( 668) hydrogen bonds : angle 7.81629 ( 1806) covalent geometry : bond 0.00463 (13770) covalent geometry : angle 1.23791 (18414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.9613 (mt) cc_final: 0.9191 (mt) REVERT: D 49 GLN cc_start: 0.9061 (tp40) cc_final: 0.8639 (mt0) REVERT: D 51 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8505 (mmmt) REVERT: D 53 MET cc_start: 0.8285 (mpp) cc_final: 0.8020 (mpp) REVERT: D 54 LEU cc_start: 0.9126 (tt) cc_final: 0.8543 (tt) REVERT: D 61 PHE cc_start: 0.8889 (t80) cc_final: 0.8673 (t80) REVERT: D 71 ARG cc_start: 0.5205 (tpp-160) cc_final: 0.4783 (tpt170) REVERT: D 80 ASN cc_start: 0.9179 (m-40) cc_final: 0.8742 (m-40) REVERT: D 97 GLN cc_start: 0.7751 (tt0) cc_final: 0.7392 (tm-30) REVERT: D 98 ILE cc_start: 0.7153 (pt) cc_final: 0.6820 (pt) REVERT: D 101 TYR cc_start: 0.7732 (t80) cc_final: 0.7520 (t80) REVERT: D 104 MET cc_start: 0.8995 (ptt) cc_final: 0.8391 (ppp) REVERT: D 105 LEU cc_start: 0.9286 (mt) cc_final: 0.9005 (mt) REVERT: D 116 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8687 (mt-10) REVERT: D 118 ARG cc_start: 0.8354 (ttt-90) cc_final: 0.7941 (ttm110) REVERT: D 142 ILE cc_start: 0.8357 (mm) cc_final: 0.7705 (mm) REVERT: D 143 PHE cc_start: 0.8900 (m-10) cc_final: 0.8368 (m-10) REVERT: D 152 LEU cc_start: 0.8079 (tp) cc_final: 0.7808 (tp) REVERT: D 168 ASN cc_start: 0.5927 (t0) cc_final: 0.4656 (t0) REVERT: D 171 LEU cc_start: 0.8993 (mt) cc_final: 0.8783 (mt) REVERT: D 178 TYR cc_start: 0.8312 (t80) cc_final: 0.7667 (t80) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1882 time to fit residues: 19.1290 Evaluate side-chains 74 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 121 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 145 optimal weight: 40.0000 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 0.0170 overall best weight: 1.3020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.123693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.106126 restraints weight = 5312.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.108687 restraints weight = 3789.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.110681 restraints weight = 2919.026| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 1.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13770 Z= 0.225 Angle : 1.270 13.868 18414 Z= 0.652 Chirality : 0.062 0.315 2070 Planarity : 0.007 0.040 2367 Dihedral : 7.983 27.179 1800 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 40.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.87 (0.19), residues: 1611 helix: -2.27 (0.13), residues: 1116 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.073 0.004 PHE G 122 TYR 0.100 0.006 TYR A 8 ARG 0.011 0.002 ARG F 33 Details of bonding type rmsd hydrogen bonds : bond 0.10629 ( 668) hydrogen bonds : angle 7.81480 ( 1806) covalent geometry : bond 0.00491 (13770) covalent geometry : angle 1.27025 (18414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: D 48 LEU cc_start: 0.9595 (mt) cc_final: 0.9196 (mt) REVERT: D 49 GLN cc_start: 0.9089 (tp40) cc_final: 0.8758 (mm110) REVERT: D 61 PHE cc_start: 0.8810 (t80) cc_final: 0.8331 (t80) REVERT: D 68 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8164 (mmt-90) REVERT: D 82 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7647 (mmt90) REVERT: D 97 GLN cc_start: 0.7739 (tt0) cc_final: 0.7518 (tm-30) REVERT: D 101 TYR cc_start: 0.7745 (t80) cc_final: 0.7541 (t80) REVERT: D 104 MET cc_start: 0.9025 (ptt) cc_final: 0.8476 (ppp) REVERT: D 105 LEU cc_start: 0.9306 (mt) cc_final: 0.9017 (mt) REVERT: D 116 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8755 (mt-10) REVERT: D 118 ARG cc_start: 0.8336 (ttt-90) cc_final: 0.7986 (ttm110) REVERT: D 133 LEU cc_start: 0.8156 (tp) cc_final: 0.7878 (tp) REVERT: D 142 ILE cc_start: 0.8396 (mm) cc_final: 0.7818 (mm) REVERT: D 143 PHE cc_start: 0.8892 (m-10) cc_final: 0.8366 (m-10) REVERT: D 152 LEU cc_start: 0.8015 (tp) cc_final: 0.7786 (tp) REVERT: D 154 GLU cc_start: 0.7594 (mp0) cc_final: 0.7050 (mm-30) REVERT: D 178 TYR cc_start: 0.8281 (t80) cc_final: 0.7176 (t80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1978 time to fit residues: 19.0476 Evaluate side-chains 73 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 18 optimal weight: 40.0000 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 126 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 0.0980 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.123298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106714 restraints weight = 5419.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109422 restraints weight = 3781.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111533 restraints weight = 2807.220| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 1.6647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13770 Z= 0.213 Angle : 1.202 12.479 18414 Z= 0.621 Chirality : 0.055 0.229 2070 Planarity : 0.007 0.047 2367 Dihedral : 7.728 25.389 1800 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 33.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.89 (0.19), residues: 1611 helix: -2.11 (0.13), residues: 1125 sheet: None (None), residues: 0 loop : -0.85 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.003 PHE A 122 TYR 0.089 0.005 TYR A 8 ARG 0.009 0.002 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.10426 ( 668) hydrogen bonds : angle 7.75133 ( 1806) covalent geometry : bond 0.00452 (13770) covalent geometry : angle 1.20155 (18414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: D 48 LEU cc_start: 0.9584 (mt) cc_final: 0.9255 (mt) REVERT: D 49 GLN cc_start: 0.9041 (tp40) cc_final: 0.8813 (mm110) REVERT: D 61 PHE cc_start: 0.8791 (t80) cc_final: 0.8400 (t80) REVERT: D 68 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8055 (mmm160) REVERT: D 69 ILE cc_start: 0.8729 (mp) cc_final: 0.8526 (mp) REVERT: D 74 LEU cc_start: 0.8698 (mt) cc_final: 0.8449 (mt) REVERT: D 104 MET cc_start: 0.9008 (ptt) cc_final: 0.8496 (ppp) REVERT: D 105 LEU cc_start: 0.9288 (mt) cc_final: 0.8976 (mt) REVERT: D 107 GLN cc_start: 0.9082 (pt0) cc_final: 0.8874 (pt0) REVERT: D 116 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8735 (tp30) REVERT: D 118 ARG cc_start: 0.8331 (ttt-90) cc_final: 0.8123 (ttm110) REVERT: D 119 SER cc_start: 0.8738 (t) cc_final: 0.7956 (m) REVERT: D 133 LEU cc_start: 0.7908 (tp) cc_final: 0.7362 (tp) REVERT: D 142 ILE cc_start: 0.8381 (mm) cc_final: 0.7799 (mm) REVERT: D 143 PHE cc_start: 0.8883 (m-10) cc_final: 0.8334 (m-10) REVERT: D 152 LEU cc_start: 0.8072 (tp) cc_final: 0.7872 (tp) REVERT: D 167 ILE cc_start: 0.7823 (pt) cc_final: 0.6803 (pt) REVERT: D 178 TYR cc_start: 0.8289 (t80) cc_final: 0.7897 (t80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1878 time to fit residues: 18.1176 Evaluate side-chains 69 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 68 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 157 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 161 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.125909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107952 restraints weight = 5147.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.110359 restraints weight = 3749.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.112348 restraints weight = 2887.338| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 1.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13770 Z= 0.213 Angle : 1.212 12.370 18414 Z= 0.628 Chirality : 0.057 0.186 2070 Planarity : 0.008 0.053 2367 Dihedral : 7.925 26.780 1800 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 33.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.88 (0.19), residues: 1611 helix: -2.13 (0.13), residues: 1125 sheet: None (None), residues: 0 loop : -0.74 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.068 0.004 PHE F 122 TYR 0.077 0.005 TYR F 8 ARG 0.009 0.002 ARG I 52 Details of bonding type rmsd hydrogen bonds : bond 0.10388 ( 668) hydrogen bonds : angle 7.85244 ( 1806) covalent geometry : bond 0.00453 (13770) covalent geometry : angle 1.21245 (18414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 LEU cc_start: 0.9552 (mt) cc_final: 0.9236 (mt) REVERT: D 49 GLN cc_start: 0.9045 (tp40) cc_final: 0.8754 (mm110) REVERT: D 68 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.8137 (mmt90) REVERT: D 102 ARG cc_start: 0.8967 (mmm-85) cc_final: 0.8366 (mmt90) REVERT: D 104 MET cc_start: 0.9049 (ptt) cc_final: 0.8469 (ppp) REVERT: D 116 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8675 (tp30) REVERT: D 118 ARG cc_start: 0.8359 (ttt-90) cc_final: 0.8145 (mtm-85) REVERT: D 119 SER cc_start: 0.8782 (t) cc_final: 0.7866 (m) REVERT: D 143 PHE cc_start: 0.8906 (m-10) cc_final: 0.8552 (m-10) REVERT: D 152 LEU cc_start: 0.7911 (tp) cc_final: 0.7638 (tp) REVERT: D 178 TYR cc_start: 0.8348 (t80) cc_final: 0.7950 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1894 time to fit residues: 17.0315 Evaluate side-chains 66 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 92 optimal weight: 0.0770 chunk 105 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 156 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 125 optimal weight: 0.1980 chunk 50 optimal weight: 0.0980 chunk 103 optimal weight: 0.3980 chunk 17 optimal weight: 0.0170 overall best weight: 0.0692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.129128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.111185 restraints weight = 5226.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113934 restraints weight = 3639.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.116030 restraints weight = 2734.374| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 1.7561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13770 Z= 0.204 Angle : 1.145 12.834 18414 Z= 0.593 Chirality : 0.054 0.187 2070 Planarity : 0.007 0.039 2367 Dihedral : 7.739 25.811 1800 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 30.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.91 (0.19), residues: 1611 helix: -2.12 (0.13), residues: 1125 sheet: None (None), residues: 0 loop : -0.86 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.003 PHE I 122 TYR 0.074 0.005 TYR B 8 ARG 0.009 0.002 ARG G 33 Details of bonding type rmsd hydrogen bonds : bond 0.10309 ( 668) hydrogen bonds : angle 7.68058 ( 1806) covalent geometry : bond 0.00443 (13770) covalent geometry : angle 1.14455 (18414) =============================================================================== Job complete usr+sys time: 3070.74 seconds wall clock time: 54 minutes 24.44 seconds (3264.44 seconds total)