Starting phenix.real_space_refine on Sat Aug 23 14:58:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2e_17362/08_2025/8p2e_17362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2e_17362/08_2025/8p2e_17362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p2e_17362/08_2025/8p2e_17362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2e_17362/08_2025/8p2e_17362.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2e_17362/08_2025/8p2e_17362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2e_17362/08_2025/8p2e_17362.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 40 5.16 5 C 8015 2.51 5 N 2180 2.21 5 O 2551 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12786 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1571 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1598 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 196} Chain: "C" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1619 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain: "D" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1598 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1596 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 11, 'TRANS': 203} Chain breaks: 1 Chain: "F" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1598 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 196} Chain: "G" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1597 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 10, 'TRANS': 204} Chain: "H" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1609 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Time building chain proxies: 3.82, per 1000 atoms: 0.30 Number of scatterers: 12786 At special positions: 0 Unit cell: (90.688, 131.456, 130.624, 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 40 16.00 O 2551 8.00 N 2180 7.00 C 8015 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: 1.21 Conformation dependent library (CDL) restraints added in 546.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3106 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 43 sheets defined 9.6% alpha, 50.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 29 through 33 Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'C' and resid 29 through 33 Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 207 through 210 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.759A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 183 through 189 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 183 through 189 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.833A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 183 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.895A pdb=" N MET A 35 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY A 51 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP A 37 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.637A pdb=" N CYS A 97 " --> pdb=" O TRP A 109 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP A 109 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG A 99 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 130 removed outlier: 5.809A pdb=" N TYR A 182 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N SER A 183 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 174 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 160 Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.550A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.550A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 49 removed outlier: 3.792A pdb=" N ASN B 53 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 114 through 118 removed outlier: 4.491A pdb=" N SER B 131 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU B 181 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL B 133 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU B 179 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.869A pdb=" N MET C 35 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY C 51 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP C 37 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.805A pdb=" N CYS C 97 " --> pdb=" O TRP C 109 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP C 109 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG C 99 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 126 through 130 removed outlier: 5.775A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 137 through 138 removed outlier: 5.775A pdb=" N TYR C 182 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 157 through 160 Processing sheet with id=AB9, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.597A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.597A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 114 through 118 removed outlier: 4.028A pdb=" N SER D 131 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU D 181 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC5, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AC6, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.845A pdb=" N MET E 35 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY E 51 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP E 37 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.691A pdb=" N CYS E 97 " --> pdb=" O TRP E 109 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRP E 109 " --> pdb=" O CYS E 97 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG E 99 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 126 through 130 removed outlier: 6.151A pdb=" N TYR E 182 " --> pdb=" O ASP E 150 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER E 183 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA E 174 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 185 " --> pdb=" O PHE E 172 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 157 through 160 Processing sheet with id=AD1, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.386A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.386A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 114 through 118 removed outlier: 4.817A pdb=" N SER F 131 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU F 181 " --> pdb=" O SER F 131 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL F 133 " --> pdb=" O LEU F 179 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU F 179 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU F 135 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER F 177 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASN F 137 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 175 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AD6, first strand: chain 'G' and resid 5 through 8 Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.152A pdb=" N GLY G 11 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET G 35 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLY G 51 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP G 37 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.152A pdb=" N GLY G 11 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N CYS G 97 " --> pdb=" O TRP G 109 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TRP G 109 " --> pdb=" O CYS G 97 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG G 99 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 126 through 130 removed outlier: 5.982A pdb=" N TYR G 182 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 137 through 138 removed outlier: 5.982A pdb=" N TYR G 182 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 156 through 160 Processing sheet with id=AE3, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.267A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.267A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.536A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 153 through 154 610 hydrogen bonds defined for protein. 1398 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: 2.24 Time building geometry restraints manager: 1.49 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: 2229 1.31 - 1.44: 3604 1.44 - 1.56: 7130 1.56 - 1.69: 66 1.69 - 1.82: 45 Bond restraints: 13074 Sorted by residual: bond pdb=" N GLU A 218 " pdb=" CA GLU A 218 " ideal model delta sigma weight residual 1.453 1.489 -0.036 8.30e-03 1.45e+04 1.84e+01 bond pdb=" CB TYR G 54 " pdb=" CG TYR G 54 " ideal model delta sigma weight residual 1.512 1.424 0.088 2.20e-02 2.07e+03 1.60e+01 bond pdb=" CB LEU F 47 " pdb=" CG LEU F 47 " ideal model delta sigma weight residual 1.530 1.451 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" CB GLN D 124 " pdb=" CG GLN D 124 " ideal model delta sigma weight residual 1.520 1.402 0.118 3.00e-02 1.11e+03 1.54e+01 bond pdb=" CB HIS B 198 " pdb=" CG HIS B 198 " ideal model delta sigma weight residual 1.497 1.443 0.054 1.40e-02 5.10e+03 1.51e+01 ... (remaining 13069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 15467 2.59 - 5.18: 2019 5.18 - 7.77: 258 7.77 - 10.35: 22 10.35 - 12.94: 6 Bond angle restraints: 17772 Sorted by residual: angle pdb=" N SER D 26 " pdb=" CA SER D 26 " pdb=" C SER D 26 " ideal model delta sigma weight residual 114.62 102.93 11.69 1.14e+00 7.69e-01 1.05e+02 angle pdb=" N ARG B 61 " pdb=" CA ARG B 61 " pdb=" C ARG B 61 " ideal model delta sigma weight residual 114.31 101.37 12.94 1.29e+00 6.01e-01 1.01e+02 angle pdb=" N ARG F 61 " pdb=" CA ARG F 61 " pdb=" C ARG F 61 " ideal model delta sigma weight residual 114.04 101.71 12.33 1.24e+00 6.50e-01 9.89e+01 angle pdb=" N SER B 26 " pdb=" CA SER B 26 " pdb=" C SER B 26 " ideal model delta sigma weight residual 114.62 103.35 11.27 1.14e+00 7.69e-01 9.78e+01 angle pdb=" N ARG D 61 " pdb=" CA ARG D 61 " pdb=" C ARG D 61 " ideal model delta sigma weight residual 114.56 103.05 11.51 1.27e+00 6.20e-01 8.21e+01 ... (remaining 17767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 7524 17.70 - 35.40: 149 35.40 - 53.10: 61 53.10 - 70.80: 29 70.80 - 88.50: 9 Dihedral angle restraints: 7772 sinusoidal: 2910 harmonic: 4862 Sorted by residual: dihedral pdb=" CD ARG H 211 " pdb=" NE ARG H 211 " pdb=" CZ ARG H 211 " pdb=" NH1 ARG H 211 " ideal model delta sinusoidal sigma weight residual 0.00 -48.89 48.89 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CA ARG D 108 " pdb=" CB ARG D 108 " pdb=" CG ARG D 108 " pdb=" CD ARG D 108 " ideal model delta sinusoidal sigma weight residual -60.00 -119.12 59.12 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP H 70 " pdb=" CB ASP H 70 " pdb=" CG ASP H 70 " pdb=" OD1 ASP H 70 " ideal model delta sinusoidal sigma weight residual -30.00 -82.62 52.62 1 2.00e+01 2.50e-03 9.43e+00 ... (remaining 7769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1330 0.084 - 0.169: 543 0.169 - 0.253: 112 0.253 - 0.337: 16 0.337 - 0.421: 5 Chirality restraints: 2006 Sorted by residual: chirality pdb=" CB VAL H 3 " pdb=" CA VAL H 3 " pdb=" CG1 VAL H 3 " pdb=" CG2 VAL H 3 " both_signs ideal model delta sigma weight residual False -2.63 -3.05 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CB VAL D 3 " pdb=" CA VAL D 3 " pdb=" CG1 VAL D 3 " pdb=" CG2 VAL D 3 " both_signs ideal model delta sigma weight residual False -2.63 -3.03 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CB VAL B 3 " pdb=" CA VAL B 3 " pdb=" CG1 VAL B 3 " pdb=" CG2 VAL B 3 " both_signs ideal model delta sigma weight residual False -2.63 -3.02 0.39 2.00e-01 2.50e+01 3.75e+00 ... (remaining 2003 not shown) Planarity restraints: 2273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 211 " 0.816 9.50e-02 1.11e+02 3.66e-01 8.12e+01 pdb=" NE ARG H 211 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG H 211 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 211 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 211 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 182 " 0.067 2.00e-02 2.50e+03 3.71e-02 2.76e+01 pdb=" CG TYR E 182 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR E 182 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 182 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR E 182 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR E 182 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR E 182 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR E 182 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 192 " -0.060 2.00e-02 2.50e+03 3.13e-02 1.96e+01 pdb=" CG TYR F 192 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR F 192 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR F 192 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR F 192 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR F 192 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR F 192 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 192 " -0.042 2.00e-02 2.50e+03 ... (remaining 2270 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 78 2.56 - 3.14: 9963 3.14 - 3.73: 20239 3.73 - 4.31: 29344 4.31 - 4.90: 47832 Nonbonded interactions: 107456 Sorted by model distance: nonbonded pdb=" O HIS H 189 " pdb=" NH1 ARG H 211 " model vdw 1.972 3.120 nonbonded pdb=" OD1 ASN H 138 " pdb=" OD1 ASP H 170 " model vdw 2.074 3.040 nonbonded pdb=" CG LYS H 190 " pdb=" NH2 ARG H 211 " model vdw 2.162 3.520 nonbonded pdb=" O PRO A 219 " pdb=" CG LYS A 220 " model vdw 2.287 3.440 nonbonded pdb=" NH1 ARG D 108 " pdb=" CG2 THR D 109 " model vdw 2.288 3.540 ... (remaining 107451 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' and (resid 4 through 28 or resid 34 through 218)) selection = (chain 'C' and (resid 4 through 28 or resid 34 through 133 or resid 141 through \ 218)) selection = (chain 'E' and (resid 4 through 133 or resid 141 through 218)) selection = (chain 'G' and (resid 4 through 28 or resid 34 through 133 or resid 141 through \ 218)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = (chain 'H' and resid 3 through 210) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.410 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 : 0.018 0.128 13074 Z= 0.951 Angle : 1.788 12.944 17772 Z= 1.199 Chirality : 0.092 0.421 2006 Planarity : 0.012 0.366 2273 Dihedral : 10.288 88.503 4666 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.92 % Favored : 97.73 % Rotamer: Outliers : 0.14 % Allowed : 0.97 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: 1.22 (0.20), residues: 1671 helix: -0.44 (0.59), residues: 64 sheet: 1.23 (0.18), residues: 769 loop : 0.64 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 61 TYR 0.067 0.009 TYR E 182 PHE 0.033 0.006 PHE B 83 TRP 0.051 0.009 TRP F 35 HIS 0.012 0.003 HIS E 170 Details of bonding type rmsd covalent geometry : bond 0.01792 (13074) covalent geometry : angle 1.78801 (17772) hydrogen bonds : bond 0.14995 ( 559) hydrogen bonds : angle 8.35112 ( 1398) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 0.527 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 PHE cc_start: 0.5067 (m-80) cc_final: 0.4667 (m-80) REVERT: A 54 TYR cc_start: 0.7960 (t80) cc_final: 0.7760 (t80) REVERT: B 29 VAL cc_start: 0.7237 (t) cc_final: 0.7033 (p) REVERT: C 78 ASN cc_start: 0.9181 (m-40) cc_final: 0.8511 (p0) REVERT: C 81 TYR cc_start: 0.7851 (m-80) cc_final: 0.6802 (m-80) REVERT: C 211 THR cc_start: 0.7555 (m) cc_final: 0.7264 (m) REVERT: C 217 VAL cc_start: 0.8022 (t) cc_final: 0.7503 (t) REVERT: D 122 ASP cc_start: 0.8376 (m-30) cc_final: 0.7936 (t0) REVERT: D 138 ASN cc_start: 0.8805 (m110) cc_final: 0.8587 (m-40) REVERT: E 60 TYR cc_start: 0.8487 (m-80) cc_final: 0.8183 (m-80) REVERT: F 31 ARG cc_start: 0.2757 (ttt180) cc_final: 0.2523 (mmt90) REVERT: F 94 THR cc_start: 0.8317 (p) cc_final: 0.7985 (t) REVERT: G 78 ASN cc_start: 0.8250 (m-40) cc_final: 0.7989 (m-40) REVERT: G 128 PHE cc_start: 0.7121 (m-80) cc_final: 0.6600 (m-80) REVERT: G 147 LEU cc_start: 0.7703 (tp) cc_final: 0.7473 (pp) REVERT: H 174 SER cc_start: 0.8720 (m) cc_final: 0.8147 (p) REVERT: H 209 PHE cc_start: 0.7899 (p90) cc_final: 0.7678 (p90) outliers start: 2 outliers final: 0 residues processed: 470 average time/residue: 0.1510 time to fit residues: 95.3851 Evaluate side-chains 237 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN C 83 GLN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN D 38 GLN D 42 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 152 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN F 89 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN H 37 GLN H 89 GLN H 124 GLN H 152 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.106592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.086413 restraints weight = 37439.980| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 4.85 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13074 Z= 0.171 Angle : 0.734 9.891 17772 Z= 0.388 Chirality : 0.046 0.226 2006 Planarity : 0.005 0.042 2273 Dihedral : 5.430 25.374 1821 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.62 % Allowed : 10.44 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: 0.97 (0.20), residues: 1671 helix: -0.37 (0.55), residues: 62 sheet: 1.23 (0.18), residues: 750 loop : 0.26 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 24 TYR 0.039 0.002 TYR D 49 PHE 0.033 0.002 PHE G 152 TRP 0.019 0.002 TRP F 96 HIS 0.005 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00378 (13074) covalent geometry : angle 0.73381 (17772) hydrogen bonds : bond 0.04763 ( 559) hydrogen bonds : angle 6.44560 ( 1398) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.528 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 SER cc_start: 0.8430 (p) cc_final: 0.8181 (t) REVERT: A 28 PHE cc_start: 0.6091 (m-80) cc_final: 0.5432 (m-80) REVERT: A 47 GLU cc_start: 0.6783 (tp30) cc_final: 0.6298 (tm-30) REVERT: A 77 LYS cc_start: 0.9071 (mtmt) cc_final: 0.8514 (ptpt) REVERT: A 81 TYR cc_start: 0.7606 (m-80) cc_final: 0.6836 (m-80) REVERT: A 121 SER cc_start: 0.7941 (p) cc_final: 0.7648 (t) REVERT: A 216 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8611 (tttm) REVERT: C 28 PHE cc_start: 0.5602 (OUTLIER) cc_final: 0.4852 (m-10) REVERT: C 78 ASN cc_start: 0.9397 (m-40) cc_final: 0.8949 (p0) REVERT: C 185 SER cc_start: 0.8777 (t) cc_final: 0.8392 (p) REVERT: C 211 THR cc_start: 0.7290 (m) cc_final: 0.6675 (p) REVERT: D 18 ARG cc_start: 0.9000 (mtp-110) cc_final: 0.8765 (mtp85) REVERT: D 70 ASP cc_start: 0.7984 (m-30) cc_final: 0.7758 (m-30) REVERT: D 103 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.6336 (ptpp) REVERT: D 122 ASP cc_start: 0.8513 (m-30) cc_final: 0.7718 (t0) REVERT: E 60 TYR cc_start: 0.8501 (m-80) cc_final: 0.8021 (m-80) REVERT: E 80 LEU cc_start: 0.8274 (tp) cc_final: 0.7947 (mm) REVERT: E 111 GLN cc_start: 0.9052 (tp40) cc_final: 0.8636 (mp10) REVERT: E 167 SER cc_start: 0.8531 (p) cc_final: 0.8305 (p) REVERT: F 94 THR cc_start: 0.8475 (p) cc_final: 0.8207 (t) REVERT: F 123 GLU cc_start: 0.8774 (pm20) cc_final: 0.8207 (pm20) REVERT: F 143 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8255 (tm-30) REVERT: F 145 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8694 (mmmm) REVERT: F 149 LYS cc_start: 0.9524 (mttt) cc_final: 0.9283 (ttmm) REVERT: G 40 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7382 (tm-30) REVERT: G 74 ASP cc_start: 0.7364 (t0) cc_final: 0.7154 (t0) REVERT: G 84 MET cc_start: 0.8363 (mtm) cc_final: 0.7915 (mtm) REVERT: G 128 PHE cc_start: 0.7811 (m-80) cc_final: 0.7011 (m-80) REVERT: G 147 LEU cc_start: 0.8026 (tp) cc_final: 0.7690 (pp) REVERT: G 186 SER cc_start: 0.8159 (t) cc_final: 0.7817 (p) REVERT: H 4 LEU cc_start: 0.7907 (mt) cc_final: 0.7650 (mt) REVERT: H 45 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7725 (ptm-80) REVERT: H 126 LYS cc_start: 0.9669 (mtmt) cc_final: 0.9404 (ptpt) REVERT: H 149 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7906 (mmmt) REVERT: H 174 SER cc_start: 0.8921 (m) cc_final: 0.8065 (p) REVERT: H 209 PHE cc_start: 0.7871 (p90) cc_final: 0.7652 (p90) outliers start: 52 outliers final: 32 residues processed: 330 average time/residue: 0.1430 time to fit residues: 64.5242 Evaluate side-chains 263 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 162 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 83 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 87 optimal weight: 0.0030 chunk 72 optimal weight: 10.0000 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 6 GLN B 138 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** G 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.100059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.080494 restraints weight = 38694.040| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 4.72 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13074 Z= 0.233 Angle : 0.718 11.987 17772 Z= 0.380 Chirality : 0.046 0.250 2006 Planarity : 0.005 0.046 2273 Dihedral : 5.317 21.103 1821 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.38 % Allowed : 12.67 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: 0.53 (0.20), residues: 1671 helix: -0.50 (0.61), residues: 64 sheet: 0.95 (0.18), residues: 759 loop : -0.07 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 99 TYR 0.026 0.002 TYR D 49 PHE 0.033 0.002 PHE E 152 TRP 0.024 0.002 TRP B 96 HIS 0.009 0.002 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00520 (13074) covalent geometry : angle 0.71807 (17772) hydrogen bonds : bond 0.04631 ( 559) hydrogen bonds : angle 6.28552 ( 1398) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 237 time to evaluate : 0.495 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 SER cc_start: 0.8441 (p) cc_final: 0.8199 (t) REVERT: A 28 PHE cc_start: 0.6407 (m-80) cc_final: 0.3839 (m-80) REVERT: A 77 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8624 (ptpt) REVERT: A 108 TYR cc_start: 0.7942 (m-80) cc_final: 0.7550 (m-80) REVERT: C 81 TYR cc_start: 0.8037 (m-80) cc_final: 0.7248 (m-10) REVERT: C 185 SER cc_start: 0.8884 (t) cc_final: 0.8552 (p) REVERT: D 89 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8194 (pp30) REVERT: D 122 ASP cc_start: 0.8666 (m-30) cc_final: 0.7798 (t0) REVERT: E 60 TYR cc_start: 0.8459 (m-80) cc_final: 0.8051 (m-80) REVERT: E 111 GLN cc_start: 0.9079 (tp40) cc_final: 0.8729 (mp10) REVERT: F 94 THR cc_start: 0.8542 (p) cc_final: 0.8208 (t) REVERT: F 143 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8348 (tm-30) REVERT: F 145 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8758 (mmmm) REVERT: F 149 LYS cc_start: 0.9618 (mttt) cc_final: 0.9336 (ttmm) REVERT: F 161 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8393 (tm-30) REVERT: G 47 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5737 (pp20) REVERT: G 74 ASP cc_start: 0.7167 (t0) cc_final: 0.6857 (t0) REVERT: G 147 LEU cc_start: 0.8307 (tp) cc_final: 0.7648 (pp) REVERT: G 212 LYS cc_start: 0.9102 (mmmm) cc_final: 0.8895 (mmmm) REVERT: H 45 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7570 (ptm-80) REVERT: H 149 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8019 (mmmt) REVERT: H 174 SER cc_start: 0.9082 (m) cc_final: 0.8824 (t) outliers start: 63 outliers final: 49 residues processed: 275 average time/residue: 0.1370 time to fit residues: 52.3738 Evaluate side-chains 253 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 194 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 33 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.101503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.082452 restraints weight = 38402.640| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.49 r_work: 0.3520 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13074 Z= 0.156 Angle : 0.635 9.212 17772 Z= 0.331 Chirality : 0.044 0.191 2006 Planarity : 0.005 0.049 2273 Dihedral : 5.008 18.883 1821 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.11 % Allowed : 13.64 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: 0.48 (0.20), residues: 1671 helix: -0.41 (0.62), residues: 62 sheet: 0.82 (0.18), residues: 773 loop : -0.02 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 99 TYR 0.017 0.002 TYR C 151 PHE 0.028 0.002 PHE G 152 TRP 0.015 0.001 TRP H 148 HIS 0.008 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00348 (13074) covalent geometry : angle 0.63511 (17772) hydrogen bonds : bond 0.03935 ( 559) hydrogen bonds : angle 6.01157 ( 1398) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 0.504 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8621 (m-30) cc_final: 0.8291 (p0) REVERT: A 77 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8648 (mtpt) REVERT: A 81 TYR cc_start: 0.8239 (m-80) cc_final: 0.8002 (m-80) REVERT: B 70 ASP cc_start: 0.8858 (m-30) cc_final: 0.8563 (m-30) REVERT: C 35 MET cc_start: 0.8118 (mmm) cc_final: 0.7807 (tpp) REVERT: C 77 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8533 (ptpp) REVERT: C 81 TYR cc_start: 0.8112 (m-80) cc_final: 0.7249 (m-10) REVERT: C 185 SER cc_start: 0.8933 (t) cc_final: 0.8681 (p) REVERT: D 71 PHE cc_start: 0.7297 (m-80) cc_final: 0.7069 (m-80) REVERT: D 122 ASP cc_start: 0.8656 (m-30) cc_final: 0.7908 (t0) REVERT: E 60 TYR cc_start: 0.8827 (m-80) cc_final: 0.8518 (m-80) REVERT: E 90 GLU cc_start: 0.7543 (pp20) cc_final: 0.7332 (pp20) REVERT: E 111 GLN cc_start: 0.9231 (tp40) cc_final: 0.8801 (mp10) REVERT: E 216 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7649 (ttpp) REVERT: F 94 THR cc_start: 0.8561 (p) cc_final: 0.8171 (t) REVERT: F 102 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7103 (t) REVERT: F 143 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8620 (tm-30) REVERT: F 145 LYS cc_start: 0.9168 (mmmt) cc_final: 0.8893 (mmmm) REVERT: F 149 LYS cc_start: 0.9607 (mttt) cc_final: 0.9267 (ttmm) REVERT: F 161 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8702 (tm-30) REVERT: G 35 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8283 (mmm) REVERT: G 47 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5699 (pp20) REVERT: G 74 ASP cc_start: 0.7366 (t0) cc_final: 0.7041 (t0) REVERT: G 147 LEU cc_start: 0.8325 (tp) cc_final: 0.7715 (pp) REVERT: G 212 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8905 (mmmm) REVERT: H 45 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7940 (ptm160) REVERT: H 149 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8068 (mmmt) outliers start: 59 outliers final: 38 residues processed: 276 average time/residue: 0.1358 time to fit residues: 51.9798 Evaluate side-chains 248 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 0.0050 chunk 26 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN H 124 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.097608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.078753 restraints weight = 39081.745| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 4.40 r_work: 0.3466 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 13074 Z= 0.226 Angle : 0.680 9.496 17772 Z= 0.356 Chirality : 0.045 0.240 2006 Planarity : 0.005 0.050 2273 Dihedral : 5.176 20.439 1821 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.31 % Allowed : 14.89 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: 0.21 (0.20), residues: 1671 helix: -0.50 (0.60), residues: 64 sheet: 0.59 (0.18), residues: 774 loop : -0.16 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 18 TYR 0.017 0.002 TYR C 33 PHE 0.032 0.002 PHE G 152 TRP 0.022 0.002 TRP E 37 HIS 0.006 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00506 (13074) covalent geometry : angle 0.67972 (17772) hydrogen bonds : bond 0.04230 ( 559) hydrogen bonds : angle 6.16823 ( 1398) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 218 time to evaluate : 0.539 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8650 (m-30) cc_final: 0.8052 (p0) REVERT: A 77 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8724 (mtpt) REVERT: B 23 CYS cc_start: 0.8089 (t) cc_final: 0.7865 (t) REVERT: B 70 ASP cc_start: 0.8954 (m-30) cc_final: 0.8645 (m-30) REVERT: C 77 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8418 (ptpp) REVERT: C 81 TYR cc_start: 0.8183 (m-80) cc_final: 0.7118 (m-80) REVERT: C 84 MET cc_start: 0.8973 (mpp) cc_final: 0.8736 (mpp) REVERT: C 108 TYR cc_start: 0.8199 (m-80) cc_final: 0.7439 (m-80) REVERT: C 111 GLN cc_start: 0.7826 (pt0) cc_final: 0.7099 (mp10) REVERT: D 71 PHE cc_start: 0.7534 (m-80) cc_final: 0.7284 (m-80) REVERT: D 122 ASP cc_start: 0.8720 (m-30) cc_final: 0.7984 (t0) REVERT: D 134 CYS cc_start: 0.8596 (t) cc_final: 0.8393 (t) REVERT: E 60 TYR cc_start: 0.8840 (m-80) cc_final: 0.8638 (m-80) REVERT: E 81 TYR cc_start: 0.8080 (m-80) cc_final: 0.7581 (m-80) REVERT: E 111 GLN cc_start: 0.9275 (tp40) cc_final: 0.8827 (mp10) REVERT: F 94 THR cc_start: 0.8623 (p) cc_final: 0.8203 (t) REVERT: F 143 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8692 (tm-30) REVERT: F 145 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8951 (mmmm) REVERT: F 149 LYS cc_start: 0.9605 (mttt) cc_final: 0.9250 (ttmm) REVERT: G 35 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8571 (mmm) REVERT: G 47 GLU cc_start: 0.6133 (OUTLIER) cc_final: 0.5870 (pp20) REVERT: G 74 ASP cc_start: 0.7130 (t0) cc_final: 0.6550 (t0) REVERT: G 81 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.6829 (m-80) REVERT: G 147 LEU cc_start: 0.8294 (tp) cc_final: 0.7662 (pp) REVERT: G 198 GLN cc_start: 0.7149 (tp40) cc_final: 0.6746 (tm-30) REVERT: G 212 LYS cc_start: 0.9250 (mmmm) cc_final: 0.8955 (mmmm) REVERT: H 23 CYS cc_start: 0.8621 (t) cc_final: 0.8251 (m) REVERT: H 24 ARG cc_start: 0.8478 (mmp80) cc_final: 0.7919 (mmp80) REVERT: H 31 ARG cc_start: 0.6817 (ttt-90) cc_final: 0.6231 (tmt-80) REVERT: H 45 ARG cc_start: 0.8132 (mtm110) cc_final: 0.7828 (ptm-80) REVERT: H 149 LYS cc_start: 0.8651 (mmmm) cc_final: 0.8164 (mmmt) outliers start: 62 outliers final: 50 residues processed: 255 average time/residue: 0.1366 time to fit residues: 48.5346 Evaluate side-chains 252 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 199 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 TYR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 144 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 96 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN G 177 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.102293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.082813 restraints weight = 37969.574| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 4.51 r_work: 0.3486 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13074 Z= 0.119 Angle : 0.619 10.197 17772 Z= 0.317 Chirality : 0.043 0.168 2006 Planarity : 0.004 0.047 2273 Dihedral : 4.705 17.859 1821 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.41 % Allowed : 16.01 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: 0.32 (0.21), residues: 1671 helix: 0.03 (0.65), residues: 62 sheet: 0.62 (0.18), residues: 782 loop : -0.08 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 18 TYR 0.015 0.001 TYR E 96 PHE 0.022 0.002 PHE G 152 TRP 0.015 0.001 TRP H 148 HIS 0.006 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00267 (13074) covalent geometry : angle 0.61871 (17772) hydrogen bonds : bond 0.03644 ( 559) hydrogen bonds : angle 5.79635 ( 1398) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.517 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8562 (m-30) cc_final: 0.8195 (p0) REVERT: A 77 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8735 (mtpt) REVERT: A 84 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7490 (mtp) REVERT: B 17 GLU cc_start: 0.7688 (tt0) cc_final: 0.7332 (tm-30) REVERT: B 70 ASP cc_start: 0.8925 (m-30) cc_final: 0.8699 (m-30) REVERT: C 35 MET cc_start: 0.8043 (mmm) cc_final: 0.7776 (tpp) REVERT: C 77 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8450 (ptpp) REVERT: C 81 TYR cc_start: 0.8137 (m-80) cc_final: 0.7251 (m-80) REVERT: C 108 TYR cc_start: 0.8165 (m-80) cc_final: 0.7487 (m-80) REVERT: C 185 SER cc_start: 0.8843 (t) cc_final: 0.8612 (p) REVERT: D 122 ASP cc_start: 0.8722 (m-30) cc_final: 0.7995 (t0) REVERT: D 134 CYS cc_start: 0.8644 (t) cc_final: 0.8442 (t) REVERT: E 81 TYR cc_start: 0.8045 (m-80) cc_final: 0.7520 (m-80) REVERT: E 111 GLN cc_start: 0.9230 (tp40) cc_final: 0.8854 (mp10) REVERT: F 94 THR cc_start: 0.8599 (p) cc_final: 0.8193 (t) REVERT: F 102 THR cc_start: 0.7388 (OUTLIER) cc_final: 0.6987 (t) REVERT: F 143 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8528 (tm-30) REVERT: F 145 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8853 (mmmm) REVERT: F 149 LYS cc_start: 0.9543 (mttt) cc_final: 0.9097 (mmmm) REVERT: G 47 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5745 (pp20) REVERT: G 74 ASP cc_start: 0.7137 (t0) cc_final: 0.6832 (t0) REVERT: G 147 LEU cc_start: 0.8270 (tp) cc_final: 0.7729 (pp) REVERT: G 198 GLN cc_start: 0.7009 (tp40) cc_final: 0.6675 (tm-30) REVERT: G 205 ASN cc_start: 0.8012 (t0) cc_final: 0.7706 (t0) REVERT: G 212 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8778 (mmmm) REVERT: H 143 GLU cc_start: 0.8406 (mp0) cc_final: 0.8111 (mp0) REVERT: H 149 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8239 (mmmt) REVERT: H 169 LYS cc_start: 0.7825 (mttt) cc_final: 0.7415 (pttp) REVERT: H 174 SER cc_start: 0.9165 (t) cc_final: 0.8687 (p) outliers start: 49 outliers final: 36 residues processed: 264 average time/residue: 0.1350 time to fit residues: 49.7263 Evaluate side-chains 248 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 16 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 210 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.097132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.077803 restraints weight = 38893.138| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 4.45 r_work: 0.3408 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 13074 Z= 0.222 Angle : 0.685 9.621 17772 Z= 0.356 Chirality : 0.045 0.246 2006 Planarity : 0.005 0.048 2273 Dihedral : 5.064 19.974 1821 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.83 % Allowed : 16.35 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: 0.02 (0.20), residues: 1671 helix: -0.77 (0.58), residues: 64 sheet: 0.46 (0.18), residues: 773 loop : -0.26 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 24 TYR 0.017 0.002 TYR E 96 PHE 0.032 0.002 PHE E 152 TRP 0.016 0.002 TRP H 148 HIS 0.007 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00500 (13074) covalent geometry : angle 0.68460 (17772) hydrogen bonds : bond 0.04097 ( 559) hydrogen bonds : angle 6.16397 ( 1398) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 0.530 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8619 (m-30) cc_final: 0.7885 (p0) REVERT: A 77 LYS cc_start: 0.9001 (mtmt) cc_final: 0.8673 (mtpt) REVERT: B 17 GLU cc_start: 0.7748 (tt0) cc_final: 0.7362 (tm-30) REVERT: B 70 ASP cc_start: 0.9004 (m-30) cc_final: 0.8755 (m-30) REVERT: B 143 GLU cc_start: 0.9231 (tp30) cc_final: 0.8829 (tp30) REVERT: C 35 MET cc_start: 0.8054 (mmm) cc_final: 0.7696 (tpp) REVERT: C 105 THR cc_start: 0.7236 (OUTLIER) cc_final: 0.6622 (p) REVERT: C 111 GLN cc_start: 0.8049 (pt0) cc_final: 0.7150 (mp10) REVERT: D 89 GLN cc_start: 0.8654 (pp30) cc_final: 0.8405 (pp30) REVERT: D 122 ASP cc_start: 0.8744 (m-30) cc_final: 0.8074 (t0) REVERT: D 134 CYS cc_start: 0.8620 (t) cc_final: 0.8414 (t) REVERT: E 111 GLN cc_start: 0.9297 (tp40) cc_final: 0.9041 (tp-100) REVERT: F 94 THR cc_start: 0.8621 (p) cc_final: 0.8138 (t) REVERT: F 143 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8661 (tm-30) REVERT: F 145 LYS cc_start: 0.9176 (mmmt) cc_final: 0.8905 (mmmm) REVERT: F 149 LYS cc_start: 0.9535 (mttt) cc_final: 0.9171 (ttmm) REVERT: F 165 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8536 (pm20) REVERT: G 47 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5889 (pp20) REVERT: G 74 ASP cc_start: 0.6923 (t0) cc_final: 0.6616 (t0) REVERT: G 198 GLN cc_start: 0.7119 (tp40) cc_final: 0.6771 (tm-30) REVERT: G 205 ASN cc_start: 0.8160 (t0) cc_final: 0.7878 (t0) REVERT: G 212 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8898 (mmmm) REVERT: H 149 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8242 (mmmt) REVERT: H 169 LYS cc_start: 0.7609 (mttt) cc_final: 0.7210 (pttp) outliers start: 55 outliers final: 44 residues processed: 242 average time/residue: 0.1356 time to fit residues: 46.0448 Evaluate side-chains 237 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 37 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.098460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.079138 restraints weight = 38370.547| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.47 r_work: 0.3445 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13074 Z= 0.155 Angle : 0.670 10.072 17772 Z= 0.342 Chirality : 0.044 0.201 2006 Planarity : 0.005 0.047 2273 Dihedral : 4.825 18.237 1821 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.41 % Allowed : 16.91 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: 0.05 (0.20), residues: 1671 helix: -0.92 (0.56), residues: 64 sheet: 0.45 (0.18), residues: 773 loop : -0.20 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 24 TYR 0.018 0.002 TYR C 81 PHE 0.027 0.002 PHE G 152 TRP 0.030 0.001 TRP H 148 HIS 0.007 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00355 (13074) covalent geometry : angle 0.66991 (17772) hydrogen bonds : bond 0.03781 ( 559) hydrogen bonds : angle 5.98735 ( 1398) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.475 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: symmetry clash revert: symmetry clash REVERT: A 49 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7407 (m) REVERT: A 74 ASP cc_start: 0.8559 (m-30) cc_final: 0.7909 (p0) REVERT: A 77 LYS cc_start: 0.8997 (mtmt) cc_final: 0.8715 (mtmt) REVERT: B 17 GLU cc_start: 0.7713 (tt0) cc_final: 0.7353 (tm-30) REVERT: B 70 ASP cc_start: 0.8992 (m-30) cc_final: 0.8771 (m-30) REVERT: C 77 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8569 (ptpp) REVERT: C 81 TYR cc_start: 0.8221 (m-80) cc_final: 0.7419 (m-80) REVERT: C 105 THR cc_start: 0.7230 (OUTLIER) cc_final: 0.6909 (p) REVERT: C 111 GLN cc_start: 0.8028 (pt0) cc_final: 0.7063 (mp10) REVERT: D 89 GLN cc_start: 0.8708 (pp30) cc_final: 0.8463 (pp30) REVERT: D 122 ASP cc_start: 0.8758 (m-30) cc_final: 0.7999 (t0) REVERT: E 81 TYR cc_start: 0.7981 (m-80) cc_final: 0.7597 (m-80) REVERT: E 111 GLN cc_start: 0.9308 (tp40) cc_final: 0.8864 (mp10) REVERT: E 205 ASN cc_start: 0.5252 (OUTLIER) cc_final: 0.4990 (t0) REVERT: F 94 THR cc_start: 0.8542 (p) cc_final: 0.8066 (t) REVERT: F 102 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7029 (t) REVERT: F 132 VAL cc_start: 0.7363 (t) cc_final: 0.7095 (m) REVERT: F 143 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8587 (tm-30) REVERT: F 145 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8892 (mmmm) REVERT: F 149 LYS cc_start: 0.9522 (mttt) cc_final: 0.9064 (mmmm) REVERT: F 165 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8485 (pm20) REVERT: G 47 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: G 74 ASP cc_start: 0.7031 (t0) cc_final: 0.6757 (t0) REVERT: G 84 MET cc_start: 0.8425 (mpp) cc_final: 0.8135 (mpp) REVERT: G 198 GLN cc_start: 0.7021 (tp40) cc_final: 0.6778 (tm-30) REVERT: G 205 ASN cc_start: 0.8168 (t0) cc_final: 0.7916 (t0) REVERT: G 212 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8925 (mmmm) REVERT: G 216 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7750 (tmtt) REVERT: H 31 ARG cc_start: 0.6836 (ttt-90) cc_final: 0.6145 (tmt-80) REVERT: H 33 LEU cc_start: 0.8130 (tt) cc_final: 0.7473 (tt) REVERT: H 70 ASP cc_start: 0.7264 (m-30) cc_final: 0.7054 (t0) REVERT: H 148 TRP cc_start: 0.7966 (m100) cc_final: 0.7750 (m100) REVERT: H 149 LYS cc_start: 0.8625 (mmmm) cc_final: 0.8223 (mmmt) REVERT: H 169 LYS cc_start: 0.7674 (mttt) cc_final: 0.7342 (pttp) outliers start: 49 outliers final: 36 residues processed: 241 average time/residue: 0.1363 time to fit residues: 45.5709 Evaluate side-chains 236 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 74 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.0000 chunk 135 optimal weight: 2.9990 chunk 149 optimal weight: 30.0000 chunk 118 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.095847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.076868 restraints weight = 39541.131| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.48 r_work: 0.3383 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 13074 Z= 0.255 Angle : 0.745 10.603 17772 Z= 0.385 Chirality : 0.046 0.224 2006 Planarity : 0.005 0.051 2273 Dihedral : 5.247 21.838 1821 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.48 % Allowed : 17.40 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: -0.27 (0.20), residues: 1671 helix: -1.02 (0.56), residues: 64 sheet: 0.19 (0.18), residues: 790 loop : -0.38 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 18 TYR 0.022 0.002 TYR E 96 PHE 0.035 0.002 PHE E 152 TRP 0.021 0.002 TRP H 148 HIS 0.006 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00574 (13074) covalent geometry : angle 0.74502 (17772) hydrogen bonds : bond 0.04254 ( 559) hydrogen bonds : angle 6.36973 ( 1398) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.519 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: symmetry clash revert: symmetry clash REVERT: B 17 GLU cc_start: 0.7720 (tt0) cc_final: 0.7346 (tm-30) REVERT: B 70 ASP cc_start: 0.9043 (m-30) cc_final: 0.8842 (m-30) REVERT: B 143 GLU cc_start: 0.9071 (tp30) cc_final: 0.8763 (tp30) REVERT: C 105 THR cc_start: 0.7286 (OUTLIER) cc_final: 0.6840 (p) REVERT: D 89 GLN cc_start: 0.8685 (pp30) cc_final: 0.8374 (pp30) REVERT: D 122 ASP cc_start: 0.8810 (m-30) cc_final: 0.8075 (t0) REVERT: E 81 TYR cc_start: 0.8008 (m-80) cc_final: 0.7444 (m-80) REVERT: E 111 GLN cc_start: 0.9367 (tp40) cc_final: 0.9104 (tp-100) REVERT: E 205 ASN cc_start: 0.5308 (OUTLIER) cc_final: 0.5027 (t0) REVERT: F 143 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8680 (tm-30) REVERT: F 145 LYS cc_start: 0.9180 (mmmt) cc_final: 0.8912 (mmmm) REVERT: F 149 LYS cc_start: 0.9537 (mttt) cc_final: 0.9240 (ttmm) REVERT: G 47 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5866 (pp20) REVERT: G 74 ASP cc_start: 0.6880 (t0) cc_final: 0.6562 (t0) REVERT: G 84 MET cc_start: 0.8558 (mpp) cc_final: 0.8333 (mpp) REVERT: G 177 GLN cc_start: 0.7729 (mt0) cc_final: 0.7506 (mt0) REVERT: G 198 GLN cc_start: 0.7215 (tp40) cc_final: 0.6950 (tm-30) REVERT: G 207 LYS cc_start: 0.8988 (tppt) cc_final: 0.8760 (mmtm) REVERT: G 212 LYS cc_start: 0.9269 (mmmm) cc_final: 0.8986 (mmmm) REVERT: G 216 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7807 (tmtt) REVERT: H 31 ARG cc_start: 0.7040 (ttt-90) cc_final: 0.6405 (tmt-80) REVERT: H 33 LEU cc_start: 0.8297 (tt) cc_final: 0.7538 (tt) REVERT: H 149 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8276 (mmmt) REVERT: H 169 LYS cc_start: 0.7495 (mttt) cc_final: 0.7191 (pttp) outliers start: 50 outliers final: 41 residues processed: 233 average time/residue: 0.1338 time to fit residues: 43.4798 Evaluate side-chains 236 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 205 ASN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 146 CYS Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 216 LYS Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 156 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 105 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.101049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.081793 restraints weight = 38592.066| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 4.49 r_work: 0.3462 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13074 Z= 0.129 Angle : 0.709 11.914 17772 Z= 0.358 Chirality : 0.044 0.175 2006 Planarity : 0.005 0.048 2273 Dihedral : 4.822 18.637 1821 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.64 % Allowed : 18.44 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: -0.10 (0.21), residues: 1671 helix: -0.91 (0.57), residues: 64 sheet: 0.26 (0.18), residues: 796 loop : -0.21 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 24 TYR 0.017 0.001 TYR H 186 PHE 0.023 0.002 PHE G 152 TRP 0.027 0.001 TRP H 148 HIS 0.006 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00298 (13074) covalent geometry : angle 0.70859 (17772) hydrogen bonds : bond 0.03711 ( 559) hydrogen bonds : angle 5.97016 ( 1398) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 0.568 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: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8948 (ptmt) cc_final: 0.8568 (pttt) REVERT: A 215 LYS cc_start: 0.8202 (tppt) cc_final: 0.7950 (tppt) REVERT: B 17 GLU cc_start: 0.7824 (tt0) cc_final: 0.7446 (tm-30) REVERT: C 105 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.6991 (p) REVERT: C 111 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7502 (pp30) REVERT: D 89 GLN cc_start: 0.8737 (pp30) cc_final: 0.8449 (pp30) REVERT: D 122 ASP cc_start: 0.8727 (m-30) cc_final: 0.7903 (t0) REVERT: D 160 GLN cc_start: 0.8313 (mp10) cc_final: 0.8015 (mp10) REVERT: E 81 TYR cc_start: 0.7952 (m-80) cc_final: 0.7456 (m-80) REVERT: E 105 THR cc_start: 0.8408 (p) cc_final: 0.8159 (p) REVERT: E 111 GLN cc_start: 0.9257 (tp40) cc_final: 0.8819 (mp10) REVERT: F 102 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.7024 (t) REVERT: F 126 LYS cc_start: 0.9471 (mmmt) cc_final: 0.9039 (pttp) REVERT: F 132 VAL cc_start: 0.7337 (t) cc_final: 0.7088 (m) REVERT: F 143 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8541 (tm-30) REVERT: F 145 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8882 (mmmm) REVERT: F 149 LYS cc_start: 0.9483 (mttt) cc_final: 0.9019 (mmmm) REVERT: F 195 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7807 (tm-30) REVERT: G 47 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5723 (pp20) REVERT: G 74 ASP cc_start: 0.7009 (t0) cc_final: 0.6697 (t0) REVERT: G 84 MET cc_start: 0.8420 (mpp) cc_final: 0.8185 (mpp) REVERT: G 212 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8861 (mmmm) REVERT: H 24 ARG cc_start: 0.7890 (mmp80) cc_final: 0.7524 (mmp-170) REVERT: H 31 ARG cc_start: 0.6844 (ttt-90) cc_final: 0.6167 (tmt-80) REVERT: H 33 LEU cc_start: 0.8130 (tt) cc_final: 0.7528 (tt) REVERT: H 148 TRP cc_start: 0.7910 (m100) cc_final: 0.7493 (m100) REVERT: H 149 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8309 (mmmt) REVERT: H 169 LYS cc_start: 0.7708 (mttt) cc_final: 0.7467 (pttp) outliers start: 38 outliers final: 31 residues processed: 237 average time/residue: 0.1347 time to fit residues: 44.9133 Evaluate side-chains 229 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 146 CYS Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 146 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.100922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081580 restraints weight = 38521.672| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 4.48 r_work: 0.3456 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.6897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13074 Z= 0.139 Angle : 0.696 13.884 17772 Z= 0.352 Chirality : 0.044 0.167 2006 Planarity : 0.005 0.050 2273 Dihedral : 4.703 19.244 1821 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.64 % Allowed : 19.00 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % 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: -0.10 (0.21), residues: 1671 helix: -0.93 (0.57), residues: 64 sheet: 0.26 (0.18), residues: 801 loop : -0.22 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 24 TYR 0.016 0.001 TYR A 182 PHE 0.023 0.002 PHE G 152 TRP 0.021 0.001 TRP H 148 HIS 0.005 0.001 HIS H 189 Details of bonding type rmsd covalent geometry : bond 0.00323 (13074) covalent geometry : angle 0.69614 (17772) hydrogen bonds : bond 0.03656 ( 559) hydrogen bonds : angle 5.85942 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3694.28 seconds wall clock time: 64 minutes 38.97 seconds (3878.97 seconds total)