Starting phenix.real_space_refine on Thu Sep 18 02:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5l08_8300/09_2025/5l08_8300.cif Found real_map, /net/cci-nas-00/data/ceres_data/5l08_8300/09_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_8300/09_2025/5l08_8300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5l08_8300/09_2025/5l08_8300.map" model { file = "/net/cci-nas-00/data/ceres_data/5l08_8300/09_2025/5l08_8300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5l08_8300/09_2025/5l08_8300.cif" } resolution = 4.6 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 ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.49, per 1000 atoms: 0.26 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: 1.17 Conformation dependent library (CDL) restraints added in 599.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.50 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: 2.20 Time building geometry restraints manager: 1.55 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: 0.01 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: 0.390 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.820 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (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 ARG 0.003 0.000 ARG A 71 TYR 0.007 0.000 TYR D 29 PHE 0.002 0.000 PHE F 45 Details of bonding type rmsd covalent geometry : bond 0.01100 (13770) covalent geometry : angle 1.03062 (18414) hydrogen bonds : bond 0.19228 ( 668) hydrogen bonds : angle 7.26414 ( 1806) *********************** 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 : 0.070 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: 0.6884 (mt) REVERT: A 40 ASP cc_start: 0.8831 (p0) cc_final: 0.8542 (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: 0.8874 (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: 0.8973 (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: 0.0988 time to fit residues: 11.3285 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 : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 9.9990 overall best weight: 1.9022 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.120255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105143 restraints weight = 5142.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107965 restraints weight = 3281.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.110144 restraints weight = 2324.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111791 restraints weight = 1742.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113025 restraints weight = 1361.249| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 1.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 13770 Z= 0.290 Angle : 1.250 17.176 18414 Z= 0.644 Chirality : 0.058 0.254 2070 Planarity : 0.015 0.199 2367 Dihedral : 7.271 24.217 1800 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.74 % Allowed : 5.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.19), residues: 1611 helix: -1.90 (0.13), residues: 1188 sheet: None (None), residues: 0 loop : 0.81 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 33 TYR 0.023 0.003 TYR A 78 PHE 0.011 0.002 PHE B 45 Details of bonding type rmsd covalent geometry : bond 0.00666 (13770) covalent geometry : angle 1.24978 (18414) hydrogen bonds : bond 0.13459 ( 668) hydrogen bonds : angle 8.76409 ( 1806) *********************** 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: 3 poor density : 114 time to evaluate : 0.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 2 ASP cc_start: 0.8271 (m-30) cc_final: 0.7965 (p0) REVERT: F 5 ARG cc_start: 0.8478 (mtt180) cc_final: 0.7876 (tpp-160) REVERT: F 24 PHE cc_start: 0.8632 (t80) cc_final: 0.8283 (t80) REVERT: F 40 ASP cc_start: 0.8405 (p0) cc_final: 0.8114 (p0) REVERT: F 44 LEU cc_start: 0.9770 (tp) cc_final: 0.9531 (tp) REVERT: F 48 LEU cc_start: 0.9517 (mt) cc_final: 0.9119 (mt) REVERT: F 54 LEU cc_start: 0.8505 (tt) cc_final: 0.8288 (tt) REVERT: F 64 GLU cc_start: 0.8392 (pt0) cc_final: 0.7864 (pt0) REVERT: F 65 LEU cc_start: 0.9133 (mm) cc_final: 0.8574 (mm) REVERT: F 67 PHE cc_start: 0.8617 (t80) cc_final: 0.7938 (t80) REVERT: F 68 ARG cc_start: 0.8899 (mmm160) cc_final: 0.7815 (mmm160) REVERT: F 76 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7823 (mt) REVERT: F 86 MET cc_start: 0.7403 (mmp) cc_final: 0.6666 (mmt) REVERT: F 107 GLN cc_start: 0.8700 (mp10) cc_final: 0.8377 (mp10) REVERT: F 133 LEU cc_start: 0.6767 (mt) cc_final: 0.6537 (mt) REVERT: F 137 MET cc_start: 0.7462 (mtt) cc_final: 0.6981 (mtt) REVERT: F 143 PHE cc_start: 0.9239 (m-10) cc_final: 0.8912 (m-10) REVERT: F 152 LEU cc_start: 0.7590 (tp) cc_final: 0.7053 (tp) REVERT: F 168 ASN cc_start: 0.5781 (t0) cc_final: 0.4844 (t0) outliers start: 3 outliers final: 0 residues processed: 115 average time/residue: 0.0922 time to fit residues: 11.4587 Evaluate side-chains 81 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 44 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 43 optimal weight: 30.0000 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 30.0000 chunk 148 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.112823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095707 restraints weight = 5421.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098111 restraints weight = 3755.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.099928 restraints weight = 2832.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101392 restraints weight = 2248.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102551 restraints weight = 1849.141| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 1.4405 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= 0.268 Angle : 1.229 13.539 18414 Z= 0.631 Chirality : 0.055 0.149 2070 Planarity : 0.010 0.127 2367 Dihedral : 7.353 25.352 1800 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 42.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.16 % Allowed : 7.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.19), residues: 1611 helix: -1.87 (0.13), residues: 1134 sheet: None (None), residues: 0 loop : -0.29 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 149 TYR 0.013 0.002 TYR H 78 PHE 0.023 0.003 PHE B 122 Details of bonding type rmsd covalent geometry : bond 0.00616 (13770) covalent geometry : angle 1.22942 (18414) hydrogen bonds : bond 0.11115 ( 668) hydrogen bonds : angle 8.47274 ( 1806) *********************** 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 107 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.067 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: 0.7996 (m-30) cc_final: 0.7544 (m-30) REVERT: F 44 LEU cc_start: 0.9759 (tp) cc_final: 0.9490 (tp) REVERT: F 48 LEU cc_start: 0.9470 (mt) cc_final: 0.9169 (mt) REVERT: F 53 MET cc_start: 0.7997 (mpp) cc_final: 0.7761 (mtm) REVERT: F 54 LEU cc_start: 0.8383 (tt) cc_final: 0.8047 (tt) REVERT: F 61 PHE cc_start: 0.8304 (t80) cc_final: 0.7466 (t80) REVERT: F 64 GLU cc_start: 0.8442 (pt0) cc_final: 0.7813 (pt0) REVERT: F 67 PHE cc_start: 0.8455 (t80) cc_final: 0.7922 (t80) REVERT: F 74 LEU cc_start: 0.9109 (mt) cc_final: 0.8428 (mt) REVERT: F 86 MET cc_start: 0.7295 (mmp) cc_final: 0.6708 (mmt) REVERT: F 97 GLN cc_start: 0.8729 (tt0) cc_final: 0.8064 (tp40) REVERT: F 142 ILE cc_start: 0.8143 (mm) cc_final: 0.7700 (mm) REVERT: F 143 PHE cc_start: 0.9244 (m-10) cc_final: 0.9027 (m-10) REVERT: F 159 ILE cc_start: 0.8709 (tp) cc_final: 0.8445 (tp) REVERT: F 168 ASN cc_start: 0.6840 (t0) cc_final: 0.5246 (t0) REVERT: F 173 LYS cc_start: 0.8794 (ptmm) cc_final: 0.8427 (mptt) REVERT: F 178 TYR cc_start: 0.8393 (t80) cc_final: 0.8135 (t80) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.0910 time to fit residues: 10.3199 Evaluate side-chains 81 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 40 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 149 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 108 optimal weight: 40.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN F 125 GLN F 166 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.114532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097645 restraints weight = 5297.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100194 restraints weight = 3581.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.102014 restraints weight = 2618.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103346 restraints weight = 2050.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104433 restraints weight = 1658.741| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 1.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 13770 Z= 0.274 Angle : 1.258 13.711 18414 Z= 0.657 Chirality : 0.063 0.250 2070 Planarity : 0.014 0.146 2367 Dihedral : 7.839 27.790 1800 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 42.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.16 % Allowed : 5.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.21), residues: 1611 helix: -1.74 (0.14), residues: 1080 sheet: None (None), residues: 0 loop : 0.39 (0.33), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG G 33 TYR 0.028 0.003 TYR F 8 PHE 0.067 0.005 PHE A 122 Details of bonding type rmsd covalent geometry : bond 0.00652 (13770) covalent geometry : angle 1.25802 (18414) hydrogen bonds : bond 0.10900 ( 668) hydrogen bonds : angle 8.35461 ( 1806) *********************** 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 94 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.066 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: 0.6847 (m-30) cc_final: 0.5981 (m-30) REVERT: F 10 ILE cc_start: 0.9106 (mm) cc_final: 0.8881 (mm) REVERT: F 44 LEU cc_start: 0.9735 (tp) cc_final: 0.9522 (tp) REVERT: F 48 LEU cc_start: 0.9604 (mt) cc_final: 0.9363 (mt) REVERT: F 74 LEU cc_start: 0.9375 (mt) cc_final: 0.9150 (mt) REVERT: F 79 LEU cc_start: 0.8174 (mm) cc_final: 0.7436 (tt) REVERT: F 97 GLN cc_start: 0.8775 (tt0) cc_final: 0.8297 (tp40) REVERT: F 115 SER cc_start: 0.9089 (t) cc_final: 0.8815 (p) REVERT: F 142 ILE cc_start: 0.8132 (mm) cc_final: 0.7740 (mm) REVERT: F 168 ASN cc_start: 0.6726 (t0) cc_final: 0.5584 (t0) REVERT: F 180 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8239 (tt0) outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.0834 time to fit residues: 8.3732 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 : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 110 optimal weight: 20.0000 chunk 126 optimal weight: 40.0000 chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 50.0000 chunk 109 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 30.0000 chunk 160 optimal weight: 7.9990 chunk 49 optimal weight: 0.0870 chunk 68 optimal weight: 6.9990 chunk 18 optimal weight: 40.0000 overall best weight: 4.2164 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.114367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098037 restraints weight = 5555.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.100683 restraints weight = 3756.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.102726 restraints weight = 2752.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.104256 restraints weight = 2130.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.105350 restraints weight = 1711.510| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 1.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 13770 Z= 0.221 Angle : 1.044 9.647 18414 Z= 0.546 Chirality : 0.051 0.167 2070 Planarity : 0.009 0.093 2367 Dihedral : 7.631 29.087 1800 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 38.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.58 % Allowed : 7.56 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.20), residues: 1611 helix: -1.82 (0.13), residues: 1098 sheet: None (None), residues: 0 loop : -0.14 (0.32), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG I 33 TYR 0.064 0.005 TYR B 8 PHE 0.014 0.003 PHE E 122 Details of bonding type rmsd covalent geometry : bond 0.00503 (13770) covalent geometry : angle 1.04367 (18414) hydrogen bonds : bond 0.09508 ( 668) hydrogen bonds : angle 7.99258 ( 1806) *********************** REFINEMENT MACRO_CYCLE 5 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 94 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.071 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: F 10 ILE cc_start: 0.9124 (mm) cc_final: 0.8906 (mm) REVERT: F 40 ASP cc_start: 0.8428 (p0) cc_final: 0.7936 (p0) REVERT: F 43 MET cc_start: 0.8985 (mpp) cc_final: 0.8704 (mmt) REVERT: F 44 LEU cc_start: 0.9710 (tp) cc_final: 0.9505 (tp) REVERT: F 48 LEU cc_start: 0.9618 (mt) cc_final: 0.9402 (mt) REVERT: F 53 MET cc_start: 0.8243 (mtm) cc_final: 0.7828 (mtm) REVERT: F 54 LEU cc_start: 0.8457 (tt) cc_final: 0.7963 (tt) REVERT: F 64 GLU cc_start: 0.8173 (pt0) cc_final: 0.7627 (pt0) REVERT: F 97 GLN cc_start: 0.8584 (tt0) cc_final: 0.8347 (tm-30) REVERT: F 142 ILE cc_start: 0.8122 (mm) cc_final: 0.7890 (mm) REVERT: F 143 PHE cc_start: 0.9256 (m-10) cc_final: 0.8949 (m-10) REVERT: F 168 ASN cc_start: 0.6797 (t0) cc_final: 0.5936 (t0) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.0943 time to fit residues: 9.4793 Evaluate side-chains 72 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 139 optimal weight: 0.0070 chunk 88 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 95 optimal weight: 0.1980 chunk 85 optimal weight: 0.0670 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 ASN F 166 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 = 0.3870 r_free = 0.3870 target = 0.122769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.103784 restraints weight = 5241.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106225 restraints weight = 3838.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108159 restraints weight = 3026.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109616 restraints weight = 2461.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.110760 restraints weight = 2082.704| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 1.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 13770 Z= 0.243 Angle : 1.202 13.164 18414 Z= 0.600 Chirality : 0.056 0.270 2070 Planarity : 0.010 0.087 2367 Dihedral : 7.496 27.061 1800 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 37.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.21), residues: 1611 helix: -2.01 (0.13), residues: 1089 sheet: None (None), residues: 0 loop : 0.12 (0.34), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 95 TYR 0.044 0.004 TYR E 8 PHE 0.026 0.003 PHE C 120 Details of bonding type rmsd covalent geometry : bond 0.00539 (13770) covalent geometry : angle 1.20229 (18414) hydrogen bonds : bond 0.09933 ( 668) hydrogen bonds : angle 7.95166 ( 1806) *********************** REFINEMENT MACRO_CYCLE 6 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 81 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 8 TYR cc_start: 0.8753 (t80) cc_final: 0.8380 (t80) REVERT: F 40 ASP cc_start: 0.8318 (p0) cc_final: 0.8117 (p0) REVERT: F 44 LEU cc_start: 0.9653 (tp) cc_final: 0.9421 (tp) REVERT: F 48 LEU cc_start: 0.9462 (mt) cc_final: 0.9213 (mt) REVERT: F 53 MET cc_start: 0.7987 (mtm) cc_final: 0.7776 (mtm) REVERT: F 54 LEU cc_start: 0.8199 (tt) cc_final: 0.7562 (tt) REVERT: F 67 PHE cc_start: 0.8151 (t80) cc_final: 0.7790 (t80) REVERT: F 68 ARG cc_start: 0.8674 (mmt-90) cc_final: 0.8321 (mpt180) REVERT: F 86 MET cc_start: 0.8147 (mmp) cc_final: 0.7282 (mmt) REVERT: F 143 PHE cc_start: 0.9174 (m-10) cc_final: 0.8857 (m-10) REVERT: F 168 ASN cc_start: 0.6897 (t0) cc_final: 0.5859 (t0) REVERT: F 173 LYS cc_start: 0.8895 (ptmm) cc_final: 0.8475 (mptt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0856 time to fit residues: 7.5582 Evaluate side-chains 63 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 148 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 151 optimal weight: 0.0770 chunk 119 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 overall best weight: 2.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 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 = 0.3892 r_free = 0.3892 target = 0.123449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.104370 restraints weight = 5146.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107046 restraints weight = 3675.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108638 restraints weight = 2841.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.110289 restraints weight = 2278.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.111378 restraints weight = 1935.569| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 1.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 13770 Z= 0.250 Angle : 1.058 12.090 18414 Z= 0.552 Chirality : 0.050 0.176 2070 Planarity : 0.020 0.301 2367 Dihedral : 7.780 36.605 1800 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 32.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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 aren not related in a simple way. whole: -2.16 (0.20), residues: 1611 helix: -1.72 (0.14), residues: 1089 sheet: None (None), residues: 0 loop : -0.26 (0.32), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 118 TYR 0.021 0.002 TYR H 8 PHE 0.018 0.002 PHE I 122 Details of bonding type rmsd covalent geometry : bond 0.00562 (13770) covalent geometry : angle 1.05789 (18414) hydrogen bonds : bond 0.09213 ( 668) hydrogen bonds : angle 7.68988 ( 1806) *********************** 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 90 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 2 ASP cc_start: 0.7658 (m-30) cc_final: 0.6420 (m-30) REVERT: D 5 ARG cc_start: 0.8685 (mpp-170) cc_final: 0.7601 (tpt170) REVERT: D 42 LEU cc_start: 0.8323 (tt) cc_final: 0.7916 (tt) REVERT: D 48 LEU cc_start: 0.9707 (mt) cc_final: 0.9360 (mt) REVERT: D 64 GLU cc_start: 0.7488 (pt0) cc_final: 0.7201 (tt0) REVERT: D 65 LEU cc_start: 0.8909 (mm) cc_final: 0.8602 (pp) REVERT: D 67 PHE cc_start: 0.7996 (t80) cc_final: 0.7227 (t80) REVERT: D 68 ARG cc_start: 0.8467 (mmt-90) cc_final: 0.7374 (mmt-90) REVERT: D 72 LEU cc_start: 0.7929 (pp) cc_final: 0.7072 (mt) REVERT: D 79 LEU cc_start: 0.7820 (mm) cc_final: 0.7617 (mm) REVERT: D 97 GLN cc_start: 0.7725 (tt0) cc_final: 0.7201 (tm-30) REVERT: D 101 TYR cc_start: 0.8144 (t80) cc_final: 0.7272 (t80) REVERT: D 137 MET cc_start: 0.7858 (mtt) cc_final: 0.7576 (mtt) REVERT: D 141 ASP cc_start: 0.8414 (m-30) cc_final: 0.8171 (m-30) REVERT: D 142 ILE cc_start: 0.8084 (mp) cc_final: 0.7457 (tp) REVERT: D 143 PHE cc_start: 0.9148 (m-10) cc_final: 0.8752 (m-10) REVERT: D 167 ILE cc_start: 0.7535 (pt) cc_final: 0.6707 (pt) REVERT: D 178 TYR cc_start: 0.8629 (t80) cc_final: 0.8289 (t80) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0882 time to fit residues: 8.6235 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 : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 11 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 109 optimal weight: 40.0000 chunk 30 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.3856 r_free = 0.3856 target = 0.123787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.102306 restraints weight = 5203.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.104962 restraints weight = 3747.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.106907 restraints weight = 2933.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108390 restraints weight = 2433.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.109406 restraints weight = 2094.773| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 1.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13770 Z= 0.250 Angle : 1.113 13.172 18414 Z= 0.579 Chirality : 0.054 0.194 2070 Planarity : 0.012 0.158 2367 Dihedral : 7.732 28.308 1800 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 32.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.19), residues: 1611 helix: -1.89 (0.13), residues: 1098 sheet: None (None), residues: 0 loop : -0.75 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 95 TYR 0.021 0.004 TYR I 8 PHE 0.023 0.002 PHE E 122 Details of bonding type rmsd covalent geometry : bond 0.00565 (13770) covalent geometry : angle 1.11272 (18414) hydrogen bonds : bond 0.09431 ( 668) hydrogen bonds : angle 7.60589 ( 1806) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 31 PRO cc_start: 0.6791 (Cg_endo) cc_final: 0.6441 (Cg_exo) REVERT: E 48 LEU cc_start: 0.9578 (mt) cc_final: 0.9318 (mt) REVERT: E 50 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8174 (tm-30) REVERT: E 53 MET cc_start: 0.8501 (mpp) cc_final: 0.8276 (mpp) REVERT: E 61 PHE cc_start: 0.8535 (t80) cc_final: 0.8064 (t80) REVERT: E 64 GLU cc_start: 0.7598 (pt0) cc_final: 0.7271 (pt0) REVERT: E 68 ARG cc_start: 0.8742 (mmt-90) cc_final: 0.7770 (mpt180) REVERT: E 86 MET cc_start: 0.8617 (mmt) cc_final: 0.8397 (mmt) REVERT: E 97 GLN cc_start: 0.8263 (tt0) cc_final: 0.7958 (tm-30) REVERT: E 98 ILE cc_start: 0.7537 (pt) cc_final: 0.7128 (pt) REVERT: E 101 TYR cc_start: 0.7834 (t80) cc_final: 0.7440 (t80) REVERT: E 106 TYR cc_start: 0.8790 (t80) cc_final: 0.8206 (t80) REVERT: E 107 GLN cc_start: 0.8677 (pm20) cc_final: 0.8449 (mp10) REVERT: E 118 ARG cc_start: 0.8774 (ttp-110) cc_final: 0.8399 (mtm-85) REVERT: E 133 LEU cc_start: 0.7759 (mt) cc_final: 0.7360 (mt) REVERT: E 137 MET cc_start: 0.7769 (mtt) cc_final: 0.7436 (mtt) REVERT: E 141 ASP cc_start: 0.8455 (m-30) cc_final: 0.8142 (m-30) REVERT: E 142 ILE cc_start: 0.8463 (mp) cc_final: 0.7901 (tp) REVERT: E 143 PHE cc_start: 0.9319 (m-10) cc_final: 0.8709 (m-10) REVERT: E 160 LEU cc_start: 0.9038 (mt) cc_final: 0.8814 (mt) REVERT: E 162 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7872 (tpt170) REVERT: E 166 GLN cc_start: 0.8598 (mm110) cc_final: 0.8287 (mm-40) REVERT: E 172 LEU cc_start: 0.9045 (mm) cc_final: 0.8526 (mt) REVERT: E 178 TYR cc_start: 0.8639 (t80) cc_final: 0.8432 (t80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0853 time to fit residues: 7.8850 Evaluate side-chains 61 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 15 optimal weight: 0.2980 chunk 132 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 153 optimal weight: 50.0000 chunk 90 optimal weight: 40.0000 chunk 85 optimal weight: 0.0370 chunk 145 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 overall best weight: 6.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.3858 r_free = 0.3858 target = 0.123494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102208 restraints weight = 5303.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104669 restraints weight = 3981.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.106508 restraints weight = 3191.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.107685 restraints weight = 2689.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.108915 restraints weight = 2365.130| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 1.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13770 Z= 0.245 Angle : 1.126 14.600 18414 Z= 0.589 Chirality : 0.051 0.161 2070 Planarity : 0.011 0.108 2367 Dihedral : 7.644 27.057 1800 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 35.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.20), residues: 1611 helix: -2.16 (0.13), residues: 1098 sheet: None (None), residues: 0 loop : -0.44 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG G 82 TYR 0.018 0.003 TYR D 101 PHE 0.024 0.003 PHE F 122 Details of bonding type rmsd covalent geometry : bond 0.00558 (13770) covalent geometry : angle 1.12584 (18414) hydrogen bonds : bond 0.09668 ( 668) hydrogen bonds : angle 7.66015 ( 1806) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 48 LEU cc_start: 0.9597 (mt) cc_final: 0.9326 (mt) REVERT: E 50 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8509 (tm-30) REVERT: E 51 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8647 (mtpp) REVERT: E 53 MET cc_start: 0.8508 (mpp) cc_final: 0.8147 (mpp) REVERT: E 64 GLU cc_start: 0.7752 (pt0) cc_final: 0.7296 (pt0) REVERT: E 68 ARG cc_start: 0.8633 (mmt-90) cc_final: 0.8302 (mpt180) REVERT: E 72 LEU cc_start: 0.7511 (pp) cc_final: 0.6779 (mt) REVERT: E 97 GLN cc_start: 0.8341 (tt0) cc_final: 0.8112 (tm-30) REVERT: E 98 ILE cc_start: 0.7866 (pt) cc_final: 0.7619 (pt) REVERT: E 101 TYR cc_start: 0.7818 (t80) cc_final: 0.7086 (t80) REVERT: E 110 GLU cc_start: 0.6254 (pt0) cc_final: 0.6026 (pt0) REVERT: E 118 ARG cc_start: 0.8808 (ttp-110) cc_final: 0.8456 (mtm-85) REVERT: E 141 ASP cc_start: 0.8604 (m-30) cc_final: 0.8378 (m-30) REVERT: E 142 ILE cc_start: 0.8346 (mp) cc_final: 0.7882 (mp) REVERT: E 143 PHE cc_start: 0.9282 (m-10) cc_final: 0.8704 (m-10) REVERT: E 166 GLN cc_start: 0.8488 (mm110) cc_final: 0.8166 (mm-40) REVERT: E 172 LEU cc_start: 0.9143 (mm) cc_final: 0.8800 (mt) REVERT: E 173 LYS cc_start: 0.9355 (ptmm) cc_final: 0.8903 (mptt) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1000 time to fit residues: 9.2949 Evaluate side-chains 67 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 13 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 149 optimal weight: 40.0000 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN E 97 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 = 0.3894 r_free = 0.3894 target = 0.126142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.104387 restraints weight = 5238.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107019 restraints weight = 3910.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109159 restraints weight = 3118.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.110759 restraints weight = 2600.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.111989 restraints weight = 2237.395| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 1.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13770 Z= 0.245 Angle : 1.159 14.572 18414 Z= 0.600 Chirality : 0.050 0.178 2070 Planarity : 0.009 0.081 2367 Dihedral : 7.665 26.067 1800 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 35.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.20), residues: 1611 helix: -2.08 (0.13), residues: 1098 sheet: None (None), residues: 0 loop : -0.38 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG E 149 TYR 0.023 0.004 TYR B 178 PHE 0.022 0.002 PHE A 122 Details of bonding type rmsd covalent geometry : bond 0.00552 (13770) covalent geometry : angle 1.15859 (18414) hydrogen bonds : bond 0.09680 ( 668) hydrogen bonds : angle 7.86789 ( 1806) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 ASP cc_start: 0.8600 (p0) cc_final: 0.7939 (p0) REVERT: E 48 LEU cc_start: 0.9530 (mt) cc_final: 0.9293 (mt) REVERT: E 50 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8532 (tm-30) REVERT: E 51 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8551 (mtpp) REVERT: E 53 MET cc_start: 0.8620 (mpp) cc_final: 0.8074 (mpp) REVERT: E 59 LEU cc_start: 0.7105 (mt) cc_final: 0.6902 (mt) REVERT: E 68 ARG cc_start: 0.8561 (mmt-90) cc_final: 0.8093 (mpt180) REVERT: E 101 TYR cc_start: 0.7570 (t80) cc_final: 0.7199 (t80) REVERT: E 106 TYR cc_start: 0.8360 (t80) cc_final: 0.8118 (t80) REVERT: E 107 GLN cc_start: 0.8765 (pm20) cc_final: 0.8380 (mp10) REVERT: E 110 GLU cc_start: 0.6315 (pt0) cc_final: 0.6027 (pt0) REVERT: E 118 ARG cc_start: 0.8810 (ttp-110) cc_final: 0.8489 (mtm-85) REVERT: E 141 ASP cc_start: 0.8692 (m-30) cc_final: 0.8327 (m-30) REVERT: E 143 PHE cc_start: 0.8903 (m-10) cc_final: 0.8445 (m-10) REVERT: E 166 GLN cc_start: 0.8416 (mm110) cc_final: 0.8086 (mm110) REVERT: E 172 LEU cc_start: 0.9126 (mm) cc_final: 0.8867 (mm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0872 time to fit residues: 8.2576 Evaluate side-chains 65 residues out of total 172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 45 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 128 optimal weight: 0.0970 chunk 46 optimal weight: 0.0000 chunk 20 optimal weight: 6.9990 chunk 159 optimal weight: 0.0370 chunk 104 optimal weight: 0.0670 chunk 42 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 97 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 = 0.3909 r_free = 0.3909 target = 0.128775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.108020 restraints weight = 5259.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.110553 restraints weight = 3973.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112416 restraints weight = 3160.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.113908 restraints weight = 2650.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.115181 restraints weight = 2289.630| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 1.7117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13770 Z= 0.223 Angle : 1.099 13.482 18414 Z= 0.574 Chirality : 0.051 0.177 2070 Planarity : 0.007 0.073 2367 Dihedral : 7.290 25.934 1800 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 29.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.19), residues: 1611 helix: -2.24 (0.13), residues: 1098 sheet: None (None), residues: 0 loop : -0.62 (0.30), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 33 TYR 0.016 0.002 TYR D 101 PHE 0.020 0.002 PHE B 122 Details of bonding type rmsd covalent geometry : bond 0.00500 (13770) covalent geometry : angle 1.09883 (18414) hydrogen bonds : bond 0.09520 ( 668) hydrogen bonds : angle 7.61189 ( 1806) =============================================================================== Job complete usr+sys time: 1535.60 seconds wall clock time: 27 minutes 49.52 seconds (1669.52 seconds total)