Starting phenix.real_space_refine on Sun Sep 13 11:59:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nj9_9384/09_2026/6nj9_9384.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nj9_9384/09_2026/6nj9_9384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nj9_9384/09_2026/6nj9_9384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nj9_9384/09_2026/6nj9_9384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nj9_9384/09_2026/6nj9_9384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nj9_9384/09_2026/6nj9_9384.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6nj9_9384/09_2026/6nj9_9384.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nj9_9384/09_2026/6nj9_9384.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 38 5.16 5 C 10962 2.51 5 N 3442 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.18s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18814 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 743 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2680 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain: "L" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Restraints were copied for chains: E, F, G, H, M, N Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N LEU N 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU N 73 " occ=0.45 Time building chain proxies: 4.32, per 1000 atoms: 0.23 Number of scatterers: 18814 At special positions: 0 Unit cell: (126.616, 175.56, 117.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 292 15.00 O 4080 8.00 N 3442 7.00 C 10962 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: 1.73 Conformation dependent library (CDL) restraints added in 577.5 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 12 sheets defined 56.0% alpha, 6.4% beta 136 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.710A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.554A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.702A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.655A pdb=" N ILE A 124 " --> pdb=" O NLE A 120 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.837A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.705A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.625A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.820A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.512A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.600A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.809A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.946A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.710A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.554A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.701A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.654A pdb=" N ILE E 124 " --> pdb=" O NLE E 120 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.837A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.705A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.625A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.819A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.512A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.601A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.809A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.946A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 48 Processing helix chain 'K' and resid 48 through 56 removed outlier: 4.144A pdb=" N LYS K 52 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 89 removed outlier: 3.760A pdb=" N MET K 71 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 119 Processing helix chain 'K' and resid 121 through 127 Processing helix chain 'K' and resid 140 through 151 Processing helix chain 'K' and resid 167 through 177 Processing helix chain 'K' and resid 189 through 210 removed outlier: 4.046A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 Processing helix chain 'K' and resid 245 through 258 removed outlier: 4.185A pdb=" N VAL K 249 " --> pdb=" O PHE K 245 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA K 258 " --> pdb=" O LYS K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 289 Processing helix chain 'K' and resid 319 through 330 removed outlier: 3.618A pdb=" N GLU K 323 " --> pdb=" O ARG K 319 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS K 330 " --> pdb=" O PHE K 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 56 through 60 Processing helix chain 'M' and resid 32 through 48 Processing helix chain 'M' and resid 48 through 56 removed outlier: 4.144A pdb=" N LYS M 52 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 89 removed outlier: 3.760A pdb=" N MET M 71 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 119 Processing helix chain 'M' and resid 121 through 127 Processing helix chain 'M' and resid 140 through 151 Processing helix chain 'M' and resid 167 through 177 Processing helix chain 'M' and resid 189 through 210 removed outlier: 4.045A pdb=" N THR M 197 " --> pdb=" O LYS M 193 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG M 200 " --> pdb=" O GLU M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 234 Processing helix chain 'M' and resid 245 through 258 removed outlier: 4.185A pdb=" N VAL M 249 " --> pdb=" O PHE M 245 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN M 252 " --> pdb=" O GLU M 248 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 289 Processing helix chain 'M' and resid 319 through 330 removed outlier: 3.617A pdb=" N GLU M 323 " --> pdb=" O ARG M 319 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS M 330 " --> pdb=" O PHE M 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.075A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.458A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.047A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 215 through 219 removed outlier: 6.448A pdb=" N HIS K 182 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU K 219 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE K 159 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL K 185 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP K 161 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL K 160 " --> pdb=" O PHE K 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.629A pdb=" N HIS L 68 " --> pdb=" O ILE L 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE L 44 " --> pdb=" O HIS L 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 215 through 219 removed outlier: 6.448A pdb=" N HIS M 182 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLU M 219 " --> pdb=" O HIS M 182 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLY M 184 " --> pdb=" O GLU M 219 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE M 159 " --> pdb=" O TYR M 183 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL M 185 " --> pdb=" O PHE M 159 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP M 161 " --> pdb=" O VAL M 185 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL M 160 " --> pdb=" O PHE M 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 12 through 16 removed outlier: 3.630A pdb=" N HIS N 68 " --> pdb=" O ILE N 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE N 44 " --> pdb=" O HIS N 68 " (cutoff:3.500A) 628 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 353 hydrogen bonds 706 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3152 1.32 - 1.44: 6259 1.44 - 1.57: 9721 1.57 - 1.69: 580 1.69 - 1.81: 68 Bond restraints: 19780 Sorted by residual: bond pdb=" N1 DC I 82 " pdb=" C6 DC I 82 " ideal model delta sigma weight residual 1.367 1.333 0.034 6.00e-03 2.78e+04 3.23e+01 bond pdb=" C3' DG J 112 " pdb=" O3' DG J 112 " ideal model delta sigma weight residual 1.435 1.367 0.068 1.30e-02 5.92e+03 2.77e+01 bond pdb=" N1 DC I 62 " pdb=" C6 DC I 62 " ideal model delta sigma weight residual 1.367 1.336 0.031 6.00e-03 2.78e+04 2.61e+01 bond pdb=" N1 DC I 92 " pdb=" C6 DC I 92 " ideal model delta sigma weight residual 1.367 1.336 0.031 6.00e-03 2.78e+04 2.61e+01 bond pdb=" N1 DC J 72 " pdb=" C6 DC J 72 " ideal model delta sigma weight residual 1.367 1.337 0.030 6.00e-03 2.78e+04 2.43e+01 ... (remaining 19775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 25841 1.92 - 3.85: 1962 3.85 - 5.77: 118 5.77 - 7.70: 45 7.70 - 9.62: 22 Bond angle restraints: 27988 Sorted by residual: angle pdb=" C LYS M 10 " pdb=" N SER M 11 " pdb=" CA SER M 11 " ideal model delta sigma weight residual 121.17 130.34 -9.17 1.62e+00 3.81e-01 3.21e+01 angle pdb=" C LYS K 10 " pdb=" N SER K 11 " pdb=" CA SER K 11 " ideal model delta sigma weight residual 121.17 130.31 -9.14 1.62e+00 3.81e-01 3.19e+01 angle pdb=" N TYR K 58 " pdb=" CA TYR K 58 " pdb=" CB TYR K 58 " ideal model delta sigma weight residual 114.17 107.91 6.26 1.14e+00 7.69e-01 3.01e+01 angle pdb=" N TYR M 58 " pdb=" CA TYR M 58 " pdb=" CB TYR M 58 " ideal model delta sigma weight residual 114.17 107.92 6.25 1.14e+00 7.69e-01 3.00e+01 angle pdb=" O4' DT I 77 " pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.86e+01 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 9531 34.83 - 69.66: 1610 69.66 - 104.50: 20 104.50 - 139.33: 0 139.33 - 174.16: 3 Dihedral angle restraints: 11164 sinusoidal: 6520 harmonic: 4644 Sorted by residual: dihedral pdb=" CA TYR K 312 " pdb=" C TYR K 312 " pdb=" N TYR K 313 " pdb=" CA TYR K 313 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TYR M 312 " pdb=" C TYR M 312 " pdb=" N TYR M 313 " pdb=" CA TYR M 313 " ideal model delta harmonic sigma weight residual 180.00 151.06 28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LYS E 37 " pdb=" C LYS E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 11161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1707 0.052 - 0.104: 1091 0.104 - 0.156: 307 0.156 - 0.207: 34 0.207 - 0.259: 7 Chirality restraints: 3146 Sorted by residual: chirality pdb=" CA TYR M 312 " pdb=" N TYR M 312 " pdb=" C TYR M 312 " pdb=" CB TYR M 312 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TYR K 312 " pdb=" N TYR K 312 " pdb=" C TYR K 312 " pdb=" CB TYR K 312 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ARG E 83 " pdb=" N ARG E 83 " pdb=" C ARG E 83 " pdb=" CB ARG E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3143 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 312 " -0.021 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR K 312 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR K 312 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR K 312 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR K 312 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR K 312 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR K 312 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 312 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 312 " 0.021 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR M 312 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR M 312 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR M 312 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR M 312 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR M 312 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR M 312 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 312 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 37 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO A 38 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " -0.045 5.00e-02 4.00e+02 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5373 2.83 - 3.35: 15463 3.35 - 3.86: 32739 3.86 - 4.38: 40851 4.38 - 4.90: 59990 Nonbonded interactions: 154416 Sorted by model distance: nonbonded pdb=" OG1 THR M 40 " pdb=" OH TYR M 209 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR K 40 " pdb=" OH TYR K 209 " model vdw 2.309 3.040 nonbonded pdb=" O SER H 123 " pdb=" OG SER H 123 " model vdw 2.314 3.040 nonbonded pdb=" O SER D 123 " pdb=" OG SER D 123 " model vdw 2.315 3.040 nonbonded pdb=" O2' SAM K 500 " pdb=" O3' SAM K 500 " model vdw 2.339 2.432 ... (remaining 154411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.810 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.015 0.111 19780 Z= 0.985 Angle : 1.077 9.623 27988 Z= 0.767 Chirality : 0.066 0.259 3146 Planarity : 0.006 0.081 2544 Dihedral : 24.716 174.160 8160 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.29 % Allowed : 5.55 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.18), residues: 1548 helix: -1.56 (0.15), residues: 824 sheet: -0.89 (0.39), residues: 162 loop : -2.28 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG N 72 TYR 0.060 0.003 TYR K 312 PHE 0.031 0.004 PHE K 68 TRP 0.009 0.002 TRP M 43 HIS 0.010 0.002 HIS N 68 Details of bonding type rmsd/Z covalent geometry : bond 0.01476 / 0.99 (19780) covalent geometry : angle 1.07750 / 0.77 (27988) hydrogen bonds : bond 0.14946 / 9.92 ( 981) hydrogen bonds : angle 5.17049 / 3.69 ( 2524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.628 Fit side-chains REVERT: C 61 GLU cc_start: 0.7988 (tp30) cc_final: 0.7744 (tp30) REVERT: D 76 GLU cc_start: 0.8110 (tp30) cc_final: 0.7823 (tp30) REVERT: G 61 GLU cc_start: 0.7995 (tp30) cc_final: 0.7758 (tp30) REVERT: G 74 LYS cc_start: 0.8522 (mttp) cc_final: 0.8319 (mttm) REVERT: H 76 GLU cc_start: 0.8035 (tp30) cc_final: 0.7768 (tp30) REVERT: K 55 MET cc_start: 0.2536 (mmm) cc_final: 0.1835 (mmt) REVERT: K 153 MET cc_start: 0.6662 (mtp) cc_final: 0.6261 (ttm) REVERT: K 201 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7963 (mm-30) REVERT: M 55 MET cc_start: 0.2473 (mmm) cc_final: 0.1752 (mmt) REVERT: M 201 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7983 (mm-30) outliers start: 4 outliers final: 3 residues processed: 191 average time/residue: 0.9421 time to fit residues: 194.5272 Evaluate side-chains 134 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 40 GLN N 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.182039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137645 restraints weight = 21202.860| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.87 r_work: 0.2832 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19780 Z= 0.155 Angle : 0.707 7.581 27988 Z= 0.393 Chirality : 0.050 0.277 3146 Planarity : 0.005 0.067 2544 Dihedral : 28.196 177.957 4966 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.17 % Allowed : 11.75 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1548 helix: 0.00 (0.17), residues: 828 sheet: -0.15 (0.41), residues: 148 loop : -1.69 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.009 0.001 TYR K 312 PHE 0.031 0.002 PHE M 68 TRP 0.007 0.001 TRP M 305 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (19780) covalent geometry : angle 0.70680 / 0.39 (27988) hydrogen bonds : bond 0.05967 / 3.89 ( 981) hydrogen bonds : angle 3.93847 / 2.83 ( 2524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.567 Fit side-chains REVERT: A 97 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8271 (mt-10) REVERT: C 99 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8166 (mmm160) REVERT: D 76 GLU cc_start: 0.8638 (tp30) cc_final: 0.8302 (tp30) REVERT: E 97 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8262 (mt-10) REVERT: H 33 ARG cc_start: 0.7451 (mmm160) cc_final: 0.7059 (mtp-110) REVERT: H 76 GLU cc_start: 0.8617 (tp30) cc_final: 0.8333 (tp30) REVERT: K 55 MET cc_start: 0.2172 (mmm) cc_final: 0.1546 (mmt) REVERT: K 153 MET cc_start: 0.6783 (mtp) cc_final: 0.6102 (ttm) REVERT: K 182 HIS cc_start: 0.8699 (m-70) cc_final: 0.8382 (m-70) REVERT: K 201 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8077 (mm-30) REVERT: M 55 MET cc_start: 0.1797 (mmm) cc_final: 0.1391 (mmt) REVERT: M 182 HIS cc_start: 0.8644 (m-70) cc_final: 0.8287 (m-70) REVERT: M 201 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8095 (mm-30) outliers start: 16 outliers final: 9 residues processed: 159 average time/residue: 0.8635 time to fit residues: 149.2909 Evaluate side-chains 143 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain M residue 207 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 79 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 144 optimal weight: 0.0770 chunk 148 optimal weight: 6.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN K 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.181108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137877 restraints weight = 21233.829| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.03 r_work: 0.2795 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19780 Z= 0.209 Angle : 0.696 6.971 27988 Z= 0.384 Chirality : 0.050 0.289 3146 Planarity : 0.006 0.060 2544 Dihedral : 28.133 178.120 4962 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.70 % Allowed : 12.55 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.21), residues: 1548 helix: 0.56 (0.18), residues: 830 sheet: -0.00 (0.44), residues: 142 loop : -1.31 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.014 0.002 TYR E 54 PHE 0.026 0.002 PHE M 68 TRP 0.007 0.001 TRP M 205 HIS 0.005 0.001 HIS K 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (19780) covalent geometry : angle 0.69567 / 0.38 (27988) hydrogen bonds : bond 0.06009 / 3.92 ( 981) hydrogen bonds : angle 3.75391 / 2.70 ( 2524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.470 Fit side-chains REVERT: C 99 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8281 (mmm160) REVERT: D 76 GLU cc_start: 0.8812 (tp30) cc_final: 0.8445 (tp30) REVERT: G 36 LYS cc_start: 0.8878 (mmtp) cc_final: 0.8557 (mtmt) REVERT: G 99 ARG cc_start: 0.8614 (mtp180) cc_final: 0.8382 (mmm160) REVERT: H 33 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7082 (mtp-110) REVERT: H 76 GLU cc_start: 0.8741 (tp30) cc_final: 0.8367 (tp30) REVERT: K 55 MET cc_start: 0.2049 (mmm) cc_final: 0.1420 (mmt) REVERT: K 153 MET cc_start: 0.6909 (mtp) cc_final: 0.6294 (ttm) REVERT: K 201 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8098 (mm-30) REVERT: K 207 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6949 (pptt) REVERT: M 55 MET cc_start: 0.2087 (mmm) cc_final: 0.1497 (mmt) REVERT: M 96 MET cc_start: 0.2568 (ptt) cc_final: 0.1632 (tpp) REVERT: M 153 MET cc_start: 0.7050 (mtp) cc_final: 0.6310 (ttm) REVERT: M 182 HIS cc_start: 0.8685 (m-70) cc_final: 0.8371 (m-70) REVERT: M 207 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6992 (pptt) outliers start: 37 outliers final: 20 residues processed: 163 average time/residue: 0.7281 time to fit residues: 130.5055 Evaluate side-chains 156 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 135 VAL Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain M residue 279 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 94 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 135 optimal weight: 0.0570 chunk 14 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.183924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.140680 restraints weight = 21200.778| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.97 r_work: 0.2853 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19780 Z= 0.131 Angle : 0.613 6.461 27988 Z= 0.346 Chirality : 0.045 0.294 3146 Planarity : 0.004 0.053 2544 Dihedral : 27.977 178.637 4962 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.19 % Allowed : 14.38 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1548 helix: 1.09 (0.18), residues: 828 sheet: 0.08 (0.46), residues: 142 loop : -1.13 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 129 TYR 0.012 0.001 TYR M 216 PHE 0.022 0.001 PHE K 68 TRP 0.006 0.001 TRP M 205 HIS 0.003 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (19780) covalent geometry : angle 0.61338 / 0.35 (27988) hydrogen bonds : bond 0.04775 / 3.11 ( 981) hydrogen bonds : angle 3.52264 / 2.55 ( 2524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.372 Fit side-chains REVERT: C 99 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8238 (mmm160) REVERT: D 33 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7243 (mtp-110) REVERT: D 76 GLU cc_start: 0.8790 (tp30) cc_final: 0.8469 (tp30) REVERT: G 36 LYS cc_start: 0.8833 (mmtp) cc_final: 0.8518 (mtmt) REVERT: G 99 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8363 (mmm160) REVERT: H 33 ARG cc_start: 0.7511 (mmm160) cc_final: 0.7091 (mtp-110) REVERT: H 76 GLU cc_start: 0.8754 (tp30) cc_final: 0.8379 (tp30) REVERT: K 55 MET cc_start: 0.1960 (mmm) cc_final: 0.1376 (mmt) REVERT: K 96 MET cc_start: 0.2281 (ptt) cc_final: 0.1624 (tpp) REVERT: K 153 MET cc_start: 0.6827 (mtp) cc_final: 0.6238 (ttm) REVERT: K 201 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8059 (mm-30) REVERT: K 207 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6941 (pptt) REVERT: M 55 MET cc_start: 0.1583 (mmm) cc_final: 0.1199 (mmt) REVERT: M 96 MET cc_start: 0.2558 (ptt) cc_final: 0.1568 (tpp) REVERT: M 153 MET cc_start: 0.6919 (mtp) cc_final: 0.6299 (ttm) REVERT: M 201 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7801 (mm-30) outliers start: 30 outliers final: 9 residues processed: 168 average time/residue: 0.7822 time to fit residues: 143.7703 Evaluate side-chains 146 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain L residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS K 251 HIS L 41 GLN M 181 HIS M 251 HIS N 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.179178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.136501 restraints weight = 21094.074| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.10 r_work: 0.2740 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 19780 Z= 0.317 Angle : 0.768 7.026 27988 Z= 0.413 Chirality : 0.055 0.297 3146 Planarity : 0.006 0.063 2544 Dihedral : 28.253 179.925 4962 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.07 % Allowed : 15.40 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.22), residues: 1548 helix: 0.76 (0.18), residues: 832 sheet: -0.01 (0.46), residues: 142 loop : -1.09 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 131 TYR 0.020 0.002 TYR E 54 PHE 0.021 0.003 PHE K 223 TRP 0.007 0.002 TRP K 205 HIS 0.007 0.001 HIS M 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.32 (19780) covalent geometry : angle 0.76827 / 0.41 (27988) hydrogen bonds : bond 0.07027 / 4.59 ( 981) hydrogen bonds : angle 3.69538 / 2.66 ( 2524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.560 Fit side-chains REVERT: C 99 ARG cc_start: 0.8546 (mmm160) cc_final: 0.8324 (mmm160) REVERT: D 76 GLU cc_start: 0.8733 (tp30) cc_final: 0.8344 (tp30) REVERT: H 76 GLU cc_start: 0.8722 (tp30) cc_final: 0.8326 (tp30) REVERT: K 55 MET cc_start: 0.1880 (mmm) cc_final: 0.1305 (mmt) REVERT: K 153 MET cc_start: 0.6937 (mtp) cc_final: 0.6240 (ttm) REVERT: K 207 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6911 (pptt) REVERT: M 55 MET cc_start: 0.1749 (mmm) cc_final: 0.1182 (mmt) REVERT: M 96 MET cc_start: 0.2253 (OUTLIER) cc_final: 0.1141 (tpp) REVERT: M 153 MET cc_start: 0.7095 (mtp) cc_final: 0.6360 (ttm) outliers start: 42 outliers final: 26 residues processed: 159 average time/residue: 0.8138 time to fit residues: 141.3553 Evaluate side-chains 159 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 34 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 206 MET Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 99 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 72 optimal weight: 30.0000 chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 145 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.180634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.137518 restraints weight = 21002.422| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.13 r_work: 0.2787 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19780 Z= 0.184 Angle : 0.681 6.651 27988 Z= 0.374 Chirality : 0.050 0.293 3146 Planarity : 0.005 0.050 2544 Dihedral : 28.195 179.028 4962 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.77 % Allowed : 15.18 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.22), residues: 1548 helix: 0.98 (0.18), residues: 834 sheet: 0.01 (0.47), residues: 142 loop : -1.05 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 129 TYR 0.014 0.002 TYR E 54 PHE 0.021 0.002 PHE M 223 TRP 0.007 0.001 TRP K 205 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (19780) covalent geometry : angle 0.68077 / 0.37 (27988) hydrogen bonds : bond 0.05746 / 3.75 ( 981) hydrogen bonds : angle 3.58929 / 2.59 ( 2524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.533 Fit side-chains REVERT: C 36 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8625 (mtmt) REVERT: D 33 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7018 (mtp-110) REVERT: D 76 GLU cc_start: 0.8736 (tp30) cc_final: 0.8336 (tp30) REVERT: G 36 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8561 (mtmt) REVERT: H 33 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7036 (mtp-110) REVERT: H 76 GLU cc_start: 0.8734 (tp30) cc_final: 0.8330 (tp30) REVERT: H 93 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: K 55 MET cc_start: 0.1810 (mmm) cc_final: 0.1208 (mmt) REVERT: K 153 MET cc_start: 0.6929 (mtp) cc_final: 0.6273 (ttm) REVERT: K 207 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6888 (pptt) REVERT: M 55 MET cc_start: 0.1720 (mmm) cc_final: 0.1160 (mmt) REVERT: M 153 MET cc_start: 0.7075 (mtp) cc_final: 0.6472 (ttm) REVERT: M 180 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7623 (mtpm) outliers start: 38 outliers final: 24 residues processed: 158 average time/residue: 0.8279 time to fit residues: 142.9088 Evaluate side-chains 166 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain K residue 198 MET Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 126 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 154 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.182186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138984 restraints weight = 21028.022| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.97 r_work: 0.2810 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19780 Z= 0.140 Angle : 0.642 6.662 27988 Z= 0.357 Chirality : 0.047 0.298 3146 Planarity : 0.005 0.046 2544 Dihedral : 28.115 178.705 4962 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.41 % Allowed : 16.28 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1548 helix: 1.26 (0.18), residues: 834 sheet: -0.00 (0.47), residues: 142 loop : -0.99 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 129 TYR 0.012 0.001 TYR E 54 PHE 0.018 0.001 PHE M 68 TRP 0.007 0.001 TRP K 205 HIS 0.004 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (19780) covalent geometry : angle 0.64196 / 0.36 (27988) hydrogen bonds : bond 0.05087 / 3.31 ( 981) hydrogen bonds : angle 3.50130 / 2.54 ( 2524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.563 Fit side-chains REVERT: C 36 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8611 (mtmt) REVERT: D 33 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6954 (mtp-110) REVERT: D 76 GLU cc_start: 0.8722 (tp30) cc_final: 0.8358 (tp30) REVERT: D 93 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: H 33 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7067 (mtp-110) REVERT: H 76 GLU cc_start: 0.8718 (tp30) cc_final: 0.8365 (tp30) REVERT: K 55 MET cc_start: 0.1781 (mmm) cc_final: 0.1193 (mmt) REVERT: K 96 MET cc_start: 0.2136 (ptt) cc_final: 0.1344 (tpp) REVERT: K 153 MET cc_start: 0.6879 (mtp) cc_final: 0.6285 (ttm) REVERT: K 207 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.6896 (pptt) REVERT: M 55 MET cc_start: 0.1473 (mmm) cc_final: 0.1127 (mmt) REVERT: M 96 MET cc_start: 0.2146 (ptt) cc_final: 0.1011 (tpp) REVERT: M 153 MET cc_start: 0.7058 (mtp) cc_final: 0.6517 (ttm) outliers start: 33 outliers final: 17 residues processed: 152 average time/residue: 0.7714 time to fit residues: 128.1285 Evaluate side-chains 157 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 109 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 0.0470 chunk 170 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 overall best weight: 1.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN L 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.182470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139477 restraints weight = 21060.971| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.05 r_work: 0.2827 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19780 Z= 0.160 Angle : 0.616 6.093 27988 Z= 0.344 Chirality : 0.046 0.308 3146 Planarity : 0.005 0.047 2544 Dihedral : 27.998 177.147 4962 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.34 % Allowed : 16.20 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1548 helix: 1.46 (0.18), residues: 834 sheet: -0.10 (0.47), residues: 142 loop : -0.89 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 129 TYR 0.015 0.001 TYR E 54 PHE 0.018 0.002 PHE M 68 TRP 0.008 0.001 TRP M 205 HIS 0.004 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (19780) covalent geometry : angle 0.61639 / 0.34 (27988) hydrogen bonds : bond 0.05003 / 3.27 ( 981) hydrogen bonds : angle 3.36122 / 2.44 ( 2524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.511 Fit side-chains REVERT: D 33 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7004 (mtp-110) REVERT: D 76 GLU cc_start: 0.8740 (tp30) cc_final: 0.8383 (tp30) REVERT: D 93 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: F 77 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8661 (mttt) REVERT: H 33 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7078 (mtp-110) REVERT: H 76 GLU cc_start: 0.8732 (tp30) cc_final: 0.8403 (tp30) REVERT: K 55 MET cc_start: 0.1825 (mmm) cc_final: 0.1220 (mmt) REVERT: K 96 MET cc_start: 0.2193 (ptt) cc_final: 0.1397 (tpp) REVERT: K 153 MET cc_start: 0.6876 (mtp) cc_final: 0.6294 (ttm) REVERT: K 207 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6906 (pptt) REVERT: M 55 MET cc_start: 0.1550 (mmm) cc_final: 0.1185 (mmt) REVERT: M 96 MET cc_start: 0.2387 (OUTLIER) cc_final: 0.1247 (tpp) REVERT: M 153 MET cc_start: 0.7010 (mtp) cc_final: 0.6698 (ttm) REVERT: M 180 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7637 (mtpm) outliers start: 32 outliers final: 19 residues processed: 156 average time/residue: 0.7621 time to fit residues: 129.9427 Evaluate side-chains 156 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain M residue 289 THR Chi-restraints excluded: chain N residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 44 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN L 41 GLN N 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.180916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137772 restraints weight = 20995.976| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.01 r_work: 0.2802 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19780 Z= 0.205 Angle : 0.661 6.133 27988 Z= 0.363 Chirality : 0.049 0.310 3146 Planarity : 0.005 0.050 2544 Dihedral : 28.099 177.230 4962 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.34 % Allowed : 16.57 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1548 helix: 1.31 (0.18), residues: 834 sheet: -0.26 (0.46), residues: 142 loop : -0.88 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 129 TYR 0.018 0.002 TYR E 54 PHE 0.019 0.002 PHE M 68 TRP 0.007 0.001 TRP M 205 HIS 0.005 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (19780) covalent geometry : angle 0.66134 / 0.36 (27988) hydrogen bonds : bond 0.05638 / 3.69 ( 981) hydrogen bonds : angle 3.40413 / 2.46 ( 2524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.632 Fit side-chains REVERT: D 33 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7084 (mtp-110) REVERT: D 76 GLU cc_start: 0.8753 (tp30) cc_final: 0.8392 (tp30) REVERT: D 93 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: H 76 GLU cc_start: 0.8741 (tp30) cc_final: 0.8391 (tp30) REVERT: K 55 MET cc_start: 0.1802 (mmm) cc_final: 0.1200 (mmt) REVERT: K 153 MET cc_start: 0.6942 (mtp) cc_final: 0.6304 (ttm) REVERT: K 155 ASP cc_start: 0.7999 (m-30) cc_final: 0.7761 (m-30) REVERT: K 207 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6924 (pptt) REVERT: M 55 MET cc_start: 0.1585 (mmm) cc_final: 0.1217 (mmt) REVERT: M 96 MET cc_start: 0.2512 (OUTLIER) cc_final: 0.1267 (tpp) REVERT: M 153 MET cc_start: 0.6974 (mtp) cc_final: 0.6635 (ttm) REVERT: M 180 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7654 (mtpm) outliers start: 32 outliers final: 20 residues processed: 158 average time/residue: 0.7617 time to fit residues: 131.5945 Evaluate side-chains 159 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain M residue 289 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 160 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 0.1980 chunk 158 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 40 GLN L 41 GLN N 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.181990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138145 restraints weight = 20925.854| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.04 r_work: 0.2807 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19780 Z= 0.142 Angle : 0.630 6.144 27988 Z= 0.350 Chirality : 0.047 0.308 3146 Planarity : 0.005 0.046 2544 Dihedral : 28.070 177.141 4962 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.75 % Allowed : 17.15 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.22), residues: 1548 helix: 1.41 (0.18), residues: 834 sheet: -0.22 (0.46), residues: 142 loop : -0.83 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 129 TYR 0.017 0.001 TYR E 54 PHE 0.017 0.002 PHE M 68 TRP 0.008 0.001 TRP M 205 HIS 0.004 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (19780) covalent geometry : angle 0.62974 / 0.35 (27988) hydrogen bonds : bond 0.05098 / 3.33 ( 981) hydrogen bonds : angle 3.38609 / 2.45 ( 2524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.477 Fit side-chains REVERT: B 77 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8607 (mttt) REVERT: D 33 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7059 (mtp-110) REVERT: D 76 GLU cc_start: 0.8729 (tp30) cc_final: 0.8330 (tp30) REVERT: H 33 ARG cc_start: 0.7450 (mmm160) cc_final: 0.7007 (mtp-110) REVERT: H 76 GLU cc_start: 0.8712 (tp30) cc_final: 0.8318 (tp30) REVERT: K 55 MET cc_start: 0.1683 (mmm) cc_final: 0.1114 (mmt) REVERT: K 153 MET cc_start: 0.6866 (mtp) cc_final: 0.6265 (ttm) REVERT: K 155 ASP cc_start: 0.7993 (m-30) cc_final: 0.7754 (m-30) REVERT: K 207 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6898 (pptt) REVERT: M 55 MET cc_start: 0.1506 (mmm) cc_final: 0.1160 (mmt) REVERT: M 96 MET cc_start: 0.2505 (OUTLIER) cc_final: 0.1272 (tpp) REVERT: M 153 MET cc_start: 0.6965 (mtp) cc_final: 0.6682 (ttm) REVERT: M 180 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7653 (mtpm) outliers start: 24 outliers final: 17 residues processed: 157 average time/residue: 0.8110 time to fit residues: 138.8822 Evaluate side-chains 157 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain M residue 289 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 73 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 123 optimal weight: 0.3980 chunk 176 optimal weight: 0.4980 chunk 134 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 41 GLN N 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139739 restraints weight = 21078.844| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.05 r_work: 0.2797 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19780 Z= 0.130 Angle : 0.615 6.147 27988 Z= 0.342 Chirality : 0.046 0.302 3146 Planarity : 0.004 0.045 2544 Dihedral : 28.022 176.494 4962 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.82 % Allowed : 17.08 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.22), residues: 1548 helix: 1.54 (0.18), residues: 834 sheet: -0.15 (0.47), residues: 140 loop : -0.82 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 129 TYR 0.012 0.001 TYR E 54 PHE 0.022 0.002 PHE K 223 TRP 0.007 0.001 TRP K 205 HIS 0.004 0.001 HIS K 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (19780) covalent geometry : angle 0.61456 / 0.34 (27988) hydrogen bonds : bond 0.04748 / 3.10 ( 981) hydrogen bonds : angle 3.31596 / 2.40 ( 2524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5140.16 seconds wall clock time: 88 minutes 12.13 seconds (5292.13 seconds total)