Starting phenix.real_space_refine on Sat Jan 18 21:22:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2e_17362/01_2025/8p2e_17362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2e_17362/01_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_17362/01_2025/8p2e_17362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2e_17362/01_2025/8p2e_17362.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2e_17362/01_2025/8p2e_17362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2e_17362/01_2025/8p2e_17362.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.36, per 1000 atoms: 0.65 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: 2.80 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 2.20 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: 4.16 Time building geometry restraints manager: 3.34 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.880 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.370 ------------------------------------------------------------------------------- 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= 1.174 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (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 TRP 0.051 0.009 TRP F 35 HIS 0.012 0.003 HIS E 170 PHE 0.033 0.006 PHE B 83 TYR 0.067 0.009 TYR E 182 ARG 0.006 0.001 ARG D 61 *********************** 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 : 1.413 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: 0.4659 (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: 0.7026 (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: 0.7502 (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: 0.7988 (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: 0.3312 time to fit residues: 207.2727 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 : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.105967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.085874 restraints weight = 37275.184| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 4.80 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13074 Z= 0.261 Angle : 0.740 9.670 17772 Z= 0.394 Chirality : 0.046 0.210 2006 Planarity : 0.005 0.042 2273 Dihedral : 5.420 24.877 1821 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.76 % Allowed : 10.51 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1671 helix: -0.37 (0.54), residues: 62 sheet: 1.24 (0.18), residues: 755 loop : 0.30 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 96 HIS 0.005 0.001 HIS A 206 PHE 0.033 0.002 PHE G 152 TYR 0.039 0.002 TYR D 49 ARG 0.007 0.001 ARG D 24 *********************** 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 348 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 1.528 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: symmetry clash REVERT: A 22 SER cc_start: 0.8439 (p) cc_final: 0.8172 (t) REVERT: A 28 PHE cc_start: 0.6118 (m-80) cc_final: 0.5427 (m-80) REVERT: A 47 GLU cc_start: 0.6819 (tp30) cc_final: 0.6522 (tm-30) REVERT: A 77 LYS cc_start: 0.9047 (mtmt) cc_final: 0.8477 (ptpt) REVERT: A 81 TYR cc_start: 0.7639 (m-80) cc_final: 0.6867 (m-80) REVERT: A 121 SER cc_start: 0.7955 (p) cc_final: 0.7665 (t) REVERT: A 216 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8607 (tttm) REVERT: C 28 PHE cc_start: 0.5552 (OUTLIER) cc_final: 0.5212 (m-10) REVERT: C 77 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8818 (mtmt) REVERT: C 78 ASN cc_start: 0.9396 (m-40) cc_final: 0.8962 (p0) REVERT: C 81 TYR cc_start: 0.8003 (m-80) cc_final: 0.6694 (m-10) REVERT: C 185 SER cc_start: 0.8776 (t) cc_final: 0.8388 (p) REVERT: D 122 ASP cc_start: 0.8526 (m-30) cc_final: 0.7695 (t0) REVERT: E 60 TYR cc_start: 0.8509 (m-80) cc_final: 0.8025 (m-80) REVERT: E 80 LEU cc_start: 0.8288 (tp) cc_final: 0.7911 (mm) REVERT: E 111 GLN cc_start: 0.9024 (tp40) cc_final: 0.8598 (mp10) REVERT: E 167 SER cc_start: 0.8534 (p) cc_final: 0.8305 (p) REVERT: F 94 THR cc_start: 0.8456 (p) cc_final: 0.8183 (t) REVERT: F 102 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7193 (t) REVERT: F 143 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8265 (tm-30) REVERT: F 145 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8687 (mmmm) REVERT: F 149 LYS cc_start: 0.9529 (mttt) cc_final: 0.9276 (ttmm) REVERT: G 40 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7408 (tm-30) REVERT: G 84 MET cc_start: 0.8337 (mtm) cc_final: 0.7873 (mtm) REVERT: G 128 PHE cc_start: 0.7819 (m-80) cc_final: 0.7059 (m-80) REVERT: G 147 LEU cc_start: 0.8036 (tp) cc_final: 0.7689 (pp) REVERT: G 186 SER cc_start: 0.8142 (t) cc_final: 0.7816 (p) REVERT: H 4 LEU cc_start: 0.7901 (mt) cc_final: 0.7647 (mt) REVERT: H 45 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7687 (ptm-80) REVERT: H 126 LYS cc_start: 0.9668 (mtmt) cc_final: 0.9406 (ptpt) REVERT: H 149 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7899 (mmmt) REVERT: H 174 SER cc_start: 0.8936 (m) cc_final: 0.8079 (p) outliers start: 54 outliers final: 33 residues processed: 326 average time/residue: 0.3077 time to fit residues: 135.4984 Evaluate side-chains 265 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 216 LYS Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR 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 60 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 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 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 149 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 106 optimal weight: 0.0070 chunk 102 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- 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 C 177 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.099948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.080226 restraints weight = 38401.243| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 4.73 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4982 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= 0.347 Angle : 0.726 11.932 17772 Z= 0.383 Chirality : 0.046 0.259 2006 Planarity : 0.005 0.047 2273 Dihedral : 5.360 21.718 1821 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.73 % Allowed : 12.25 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1671 helix: -0.46 (0.57), residues: 64 sheet: 0.96 (0.18), residues: 776 loop : -0.02 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 96 HIS 0.008 0.002 HIS H 189 PHE 0.033 0.002 PHE E 152 TYR 0.023 0.002 TYR D 49 ARG 0.007 0.001 ARG A 99 *********************** 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 303 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 1.418 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: A 22 SER cc_start: 0.8390 (p) cc_final: 0.8111 (t) REVERT: A 28 PHE cc_start: 0.6375 (m-80) cc_final: 0.5336 (m-80) REVERT: A 77 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8563 (ptpt) REVERT: A 108 TYR cc_start: 0.7939 (m-80) cc_final: 0.7613 (m-80) REVERT: C 185 SER cc_start: 0.8898 (t) cc_final: 0.8580 (p) REVERT: D 89 GLN cc_start: 0.8516 (pp30) cc_final: 0.8123 (pp30) REVERT: D 122 ASP cc_start: 0.8625 (m-30) cc_final: 0.7823 (t0) REVERT: E 60 TYR cc_start: 0.8459 (m-80) cc_final: 0.8045 (m-80) REVERT: E 111 GLN cc_start: 0.9080 (tp40) cc_final: 0.8733 (mp10) REVERT: F 75 ILE cc_start: 0.8926 (mt) cc_final: 0.8652 (mt) REVERT: F 94 THR cc_start: 0.8547 (p) cc_final: 0.8205 (t) REVERT: F 143 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8353 (tm-30) REVERT: F 145 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8731 (mmmm) REVERT: F 149 LYS cc_start: 0.9619 (mttt) cc_final: 0.9316 (ttmm) REVERT: F 161 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8414 (tm-30) REVERT: G 47 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5657 (pp20) REVERT: G 74 ASP cc_start: 0.7360 (t0) cc_final: 0.7005 (t70) REVERT: G 81 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: G 147 LEU cc_start: 0.8305 (tp) cc_final: 0.7622 (pp) REVERT: G 154 GLU cc_start: 0.8078 (tt0) cc_final: 0.7823 (tt0) REVERT: G 212 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8856 (mmmm) REVERT: H 149 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8050 (mmmt) REVERT: H 174 SER cc_start: 0.9102 (m) cc_final: 0.8865 (t) outliers start: 68 outliers final: 51 residues processed: 278 average time/residue: 0.2882 time to fit residues: 111.1041 Evaluate side-chains 260 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 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 135 LEU 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 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 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 81 TYR 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 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 92 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 39 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 102 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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** ** F 198 HIS ** 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 = 0.4028 r_free = 0.4028 target = 0.100306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.080614 restraints weight = 37842.507| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 4.68 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13074 Z= 0.279 Angle : 0.656 9.070 17772 Z= 0.343 Chirality : 0.044 0.207 2006 Planarity : 0.005 0.049 2273 Dihedral : 5.097 19.878 1821 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.31 % Allowed : 13.71 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1671 helix: -0.36 (0.60), residues: 64 sheet: 0.80 (0.18), residues: 765 loop : -0.06 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 148 HIS 0.008 0.001 HIS H 189 PHE 0.031 0.002 PHE G 152 TYR 0.017 0.002 TYR C 151 ARG 0.005 0.001 ARG G 88 *********************** 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 295 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 1.426 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: A 22 SER cc_start: 0.8362 (p) cc_final: 0.8123 (t) REVERT: A 35 MET cc_start: 0.8422 (mmp) cc_final: 0.8170 (mmp) REVERT: A 74 ASP cc_start: 0.8473 (m-30) cc_final: 0.7944 (p0) REVERT: A 77 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8649 (mtpt) REVERT: B 23 CYS cc_start: 0.7821 (t) cc_final: 0.7393 (t) REVERT: B 70 ASP cc_start: 0.8913 (m-30) cc_final: 0.8595 (m-30) REVERT: C 77 LYS cc_start: 0.9099 (mtmt) cc_final: 0.8671 (ptpp) REVERT: C 81 TYR cc_start: 0.8171 (m-80) cc_final: 0.7302 (m-10) REVERT: C 185 SER cc_start: 0.8907 (t) cc_final: 0.8602 (p) REVERT: D 89 GLN cc_start: 0.8503 (pp30) cc_final: 0.8103 (pp30) REVERT: D 122 ASP cc_start: 0.8634 (m-30) cc_final: 0.7799 (t0) REVERT: E 60 TYR cc_start: 0.8472 (m-80) cc_final: 0.8096 (m-80) REVERT: E 90 GLU cc_start: 0.7375 (pp20) cc_final: 0.7157 (pp20) REVERT: E 111 GLN cc_start: 0.9135 (tp40) cc_final: 0.8718 (mp10) REVERT: F 75 ILE cc_start: 0.8910 (mt) cc_final: 0.8635 (mt) REVERT: F 94 THR cc_start: 0.8592 (p) cc_final: 0.8244 (t) REVERT: F 143 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8280 (tm-30) REVERT: F 145 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8771 (mmmm) REVERT: F 149 LYS cc_start: 0.9650 (mttt) cc_final: 0.9335 (ttmm) REVERT: F 161 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8434 (tm-30) REVERT: G 35 MET cc_start: 0.8651 (mmm) cc_final: 0.8338 (mmm) REVERT: G 47 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5531 (pp20) REVERT: G 74 ASP cc_start: 0.7175 (t0) cc_final: 0.6688 (t70) REVERT: G 81 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: G 147 LEU cc_start: 0.8308 (tp) cc_final: 0.7635 (pp) REVERT: G 212 LYS cc_start: 0.9118 (mmmm) cc_final: 0.8747 (mmmm) REVERT: H 45 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7691 (ptm160) REVERT: H 149 LYS cc_start: 0.8468 (mmmm) cc_final: 0.7986 (mmmt) REVERT: H 174 SER cc_start: 0.8995 (m) cc_final: 0.8782 (t) outliers start: 62 outliers final: 46 residues processed: 272 average time/residue: 0.2877 time to fit residues: 107.9366 Evaluate side-chains 256 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 B residue 185 ASP 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 92 ILE Chi-restraints excluded: chain D residue 152 ASN 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 58 ASP Chi-restraints excluded: chain E residue 65 VAL 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 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 211 THR Chi-restraints excluded: chain G residue 213 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 112 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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** ** 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3948 r_free = 0.3948 target = 0.093520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.075021 restraints weight = 39519.452| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 4.32 r_work: 0.3410 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.131 13074 Z= 0.608 Angle : 0.852 9.685 17772 Z= 0.454 Chirality : 0.050 0.333 2006 Planarity : 0.006 0.057 2273 Dihedral : 6.158 28.003 1821 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.22 % Allowed : 13.78 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1671 helix: -0.85 (0.59), residues: 64 sheet: 0.13 (0.18), residues: 781 loop : -0.67 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 96 HIS 0.007 0.002 HIS H 189 PHE 0.048 0.004 PHE E 152 TYR 0.026 0.003 TYR C 96 ARG 0.007 0.001 ARG A 99 *********************** 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 287 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 212 time to evaluate : 1.386 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 22 SER cc_start: 0.8631 (p) cc_final: 0.8378 (t) REVERT: A 77 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8616 (ptpt) REVERT: B 17 GLU cc_start: 0.7674 (tt0) cc_final: 0.7351 (tm-30) REVERT: B 70 ASP cc_start: 0.8962 (m-30) cc_final: 0.8713 (m-30) REVERT: C 28 PHE cc_start: 0.5450 (m-10) cc_final: 0.4723 (m-10) REVERT: C 71 ILE cc_start: 0.8909 (tt) cc_final: 0.8695 (tp) REVERT: C 81 TYR cc_start: 0.8367 (m-80) cc_final: 0.7368 (m-80) REVERT: C 84 MET cc_start: 0.9020 (mpp) cc_final: 0.8810 (mpp) REVERT: C 108 TYR cc_start: 0.8136 (m-80) cc_final: 0.7818 (m-80) REVERT: D 70 ASP cc_start: 0.8461 (m-30) cc_final: 0.8154 (m-30) REVERT: D 71 PHE cc_start: 0.7947 (m-80) cc_final: 0.7727 (m-80) REVERT: D 89 GLN cc_start: 0.8634 (pp30) cc_final: 0.8254 (pp30) REVERT: D 122 ASP cc_start: 0.8764 (m-30) cc_final: 0.8022 (t0) REVERT: E 60 TYR cc_start: 0.8714 (m-80) cc_final: 0.8427 (m-80) REVERT: F 143 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8789 (tm-30) REVERT: F 145 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8983 (mmmm) REVERT: F 149 LYS cc_start: 0.9619 (mttt) cc_final: 0.9155 (mtpp) REVERT: G 35 MET cc_start: 0.9080 (mmm) cc_final: 0.8762 (mmm) REVERT: G 81 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: G 177 GLN cc_start: 0.7886 (mt0) cc_final: 0.7648 (mt0) REVERT: G 212 LYS cc_start: 0.9243 (mmmm) cc_final: 0.9001 (mmmm) REVERT: H 149 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8336 (mmmt) REVERT: H 152 ASN cc_start: 0.9613 (t0) cc_final: 0.9404 (t0) outliers start: 75 outliers final: 60 residues processed: 261 average time/residue: 0.2801 time to fit residues: 101.6623 Evaluate side-chains 256 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 54 TYR 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 91 ASP 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 199 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 48 ILE 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 B residue 185 ASP Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 197 THR 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 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 38 VAL Chi-restraints excluded: chain E residue 49 VAL 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 92 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 190 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 13 VAL 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 81 TYR 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 213 VAL 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 31 optimal weight: 0.2980 chunk 121 optimal weight: 0.8980 chunk 148 optimal weight: 7.9990 chunk 66 optimal weight: 0.0060 chunk 80 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 14 optimal weight: 0.0370 chunk 8 optimal weight: 0.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- 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** A 210 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 111 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.099617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.080308 restraints weight = 38211.145| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 4.47 r_work: 0.3464 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13074 Z= 0.175 Angle : 0.645 9.312 17772 Z= 0.331 Chirality : 0.044 0.167 2006 Planarity : 0.005 0.049 2273 Dihedral : 5.015 20.893 1821 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.51 % Allowed : 16.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1671 helix: -0.41 (0.62), residues: 64 sheet: 0.40 (0.18), residues: 761 loop : -0.38 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 148 HIS 0.007 0.001 HIS H 189 PHE 0.027 0.002 PHE B 139 TYR 0.017 0.001 TYR A 54 ARG 0.005 0.001 ARG H 31 *********************** 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 259 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 1.512 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: A 74 ASP cc_start: 0.8456 (m-30) cc_final: 0.7833 (p0) REVERT: A 77 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8530 (mtmt) REVERT: B 147 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: C 77 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8370 (ptpp) REVERT: C 81 TYR cc_start: 0.8284 (m-80) cc_final: 0.7322 (m-80) REVERT: C 84 MET cc_start: 0.8956 (mpp) cc_final: 0.8729 (mpp) REVERT: C 111 GLN cc_start: 0.8982 (tp40) cc_final: 0.7655 (mp10) REVERT: D 70 ASP cc_start: 0.8501 (m-30) cc_final: 0.8269 (m-30) REVERT: D 89 GLN cc_start: 0.8755 (pp30) cc_final: 0.8403 (pp30) REVERT: D 122 ASP cc_start: 0.8722 (m-30) cc_final: 0.7972 (t0) REVERT: E 90 GLU cc_start: 0.7661 (pp20) cc_final: 0.7438 (pp20) REVERT: E 105 THR cc_start: 0.8351 (p) cc_final: 0.8053 (p) REVERT: E 111 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8806 (mp10) REVERT: E 212 LYS cc_start: 0.8114 (tppt) cc_final: 0.7867 (tppt) REVERT: F 102 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.6995 (t) REVERT: F 143 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8595 (tm-30) REVERT: F 145 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8851 (mmmm) REVERT: F 149 LYS cc_start: 0.9566 (mttt) cc_final: 0.9097 (mmmm) REVERT: G 74 ASP cc_start: 0.7368 (t0) cc_final: 0.7118 (t0) REVERT: G 205 ASN cc_start: 0.8187 (t0) cc_final: 0.7968 (t0) REVERT: G 212 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8819 (mmmm) REVERT: G 216 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7812 (tmtt) REVERT: H 31 ARG cc_start: 0.6841 (ttt-90) cc_final: 0.6038 (tmt-80) REVERT: H 33 LEU cc_start: 0.8070 (tt) cc_final: 0.7605 (tt) REVERT: H 123 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8436 (tp30) REVERT: H 149 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8249 (mmmt) outliers start: 36 outliers final: 24 residues processed: 248 average time/residue: 0.2962 time to fit residues: 101.5968 Evaluate side-chains 230 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE 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 217 VAL Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 146 CYS 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 111 GLN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 102 THR 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 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 114 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN E 170 HIS E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** 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 = 0.3934 r_free = 0.3934 target = 0.094672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075551 restraints weight = 39520.148| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 4.46 r_work: 0.3363 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 13074 Z= 0.426 Angle : 0.734 8.879 17772 Z= 0.387 Chirality : 0.046 0.261 2006 Planarity : 0.006 0.058 2273 Dihedral : 5.466 22.887 1821 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.97 % Allowed : 16.14 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1671 helix: -0.86 (0.56), residues: 64 sheet: 0.18 (0.18), residues: 774 loop : -0.50 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 148 HIS 0.007 0.001 HIS H 189 PHE 0.035 0.003 PHE E 152 TYR 0.020 0.002 TYR C 96 ARG 0.008 0.001 ARG A 99 *********************** 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: 57 poor density : 203 time to evaluate : 1.466 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 77 LYS cc_start: 0.9019 (mtmt) cc_final: 0.8580 (ptpt) REVERT: B 17 GLU cc_start: 0.7880 (tt0) cc_final: 0.7344 (tm-30) REVERT: B 70 ASP cc_start: 0.8819 (m-30) cc_final: 0.8519 (t0) REVERT: B 147 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7720 (mt0) REVERT: C 81 TYR cc_start: 0.8421 (m-80) cc_final: 0.7772 (m-80) REVERT: C 105 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6698 (p) REVERT: D 89 GLN cc_start: 0.8738 (pp30) cc_final: 0.8297 (pp30) REVERT: D 122 ASP cc_start: 0.8774 (m-30) cc_final: 0.8038 (t0) REVERT: E 111 GLN cc_start: 0.9282 (OUTLIER) cc_final: 0.8981 (mp10) REVERT: F 143 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8770 (tm-30) REVERT: G 81 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: G 84 MET cc_start: 0.8629 (mpp) cc_final: 0.8368 (mpp) REVERT: G 205 ASN cc_start: 0.8272 (t0) cc_final: 0.7960 (t0) REVERT: G 212 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8891 (mmmm) REVERT: G 216 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8065 (tmtt) REVERT: H 31 ARG cc_start: 0.7069 (ttt-90) cc_final: 0.6406 (tmt-80) REVERT: H 149 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8303 (mmmt) outliers start: 57 outliers final: 40 residues processed: 241 average time/residue: 0.2950 time to fit residues: 98.6313 Evaluate side-chains 241 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE 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 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain C residue 60 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 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 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 111 GLN 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 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 81 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.2709 > 50: distance: 0 - 1: 13.293 distance: 1 - 2: 12.097 distance: 1 - 4: 8.675 distance: 2 - 3: 11.619 distance: 2 - 7: 21.510 distance: 4 - 5: 8.271 distance: 4 - 6: 8.731 distance: 7 - 8: 20.091 distance: 8 - 9: 11.303 distance: 8 - 11: 11.740 distance: 9 - 10: 16.715 distance: 9 - 15: 10.643 distance: 11 - 12: 15.194 distance: 12 - 13: 11.315 distance: 12 - 14: 16.193 distance: 15 - 16: 13.396 distance: 15 - 102: 23.721 distance: 16 - 17: 8.572 distance: 16 - 19: 7.881 distance: 17 - 18: 5.602 distance: 17 - 22: 4.540 distance: 18 - 99: 7.286 distance: 19 - 20: 8.149 distance: 19 - 21: 10.819 distance: 22 - 23: 4.889 distance: 23 - 24: 14.414 distance: 23 - 26: 4.789 distance: 24 - 25: 21.273 distance: 24 - 31: 11.441 distance: 26 - 27: 9.219 distance: 27 - 28: 4.306 distance: 28 - 29: 11.101 distance: 28 - 30: 6.535 distance: 31 - 32: 5.560 distance: 31 - 90: 9.471 distance: 32 - 33: 10.471 distance: 32 - 35: 12.084 distance: 33 - 34: 21.227 distance: 33 - 37: 20.060 distance: 34 - 87: 18.332 distance: 35 - 36: 17.895 distance: 37 - 38: 20.116 distance: 37 - 43: 10.417 distance: 38 - 39: 26.822 distance: 38 - 41: 27.167 distance: 39 - 40: 26.774 distance: 39 - 44: 44.625 distance: 41 - 42: 22.764 distance: 42 - 43: 17.572 distance: 44 - 45: 52.603 distance: 45 - 46: 20.525 distance: 45 - 48: 34.530 distance: 46 - 47: 19.918 distance: 46 - 49: 9.954 distance: 49 - 50: 22.778 distance: 50 - 51: 21.496 distance: 50 - 53: 18.707 distance: 51 - 52: 8.033 distance: 51 - 56: 8.217 distance: 53 - 54: 8.999 distance: 53 - 55: 17.265 distance: 56 - 57: 21.836 distance: 57 - 58: 26.026 distance: 57 - 60: 29.331 distance: 58 - 59: 14.649 distance: 58 - 64: 15.188 distance: 60 - 61: 14.700 distance: 61 - 62: 7.218 distance: 61 - 63: 29.250