Starting phenix.real_space_refine on Wed Jul 30 22:42:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p2e_17362/07_2025/8p2e_17362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p2e_17362/07_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_17362/07_2025/8p2e_17362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p2e_17362/07_2025/8p2e_17362.map" model { file = "/net/cci-nas-00/data/ceres_data/8p2e_17362/07_2025/8p2e_17362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p2e_17362/07_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.69, per 1000 atoms: 0.68 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: 2.98 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: 2.36 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: 4.31 Time building geometry restraints manager: 3.57 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: 3.860 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.270 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.570 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.14995 ( 559) hydrogen bonds : angle 8.35112 ( 1398) covalent geometry : bond 0.01792 (13074) covalent geometry : angle 1.78801 (17772) *********************** 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 : 1.323 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: 0.3140 time to fit residues: 196.8915 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 : 1.421 ------------------------------------------------------------------------------- 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 = 0.105966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.085874 restraints weight = 37274.014| |-----------------------------------------------------------------------------| 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= 0.181 Angle : 0.740 9.671 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 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 559) hydrogen bonds : angle 6.45878 ( 1398) covalent geometry : bond 0.00401 (13074) covalent geometry : angle 0.73960 (17772) *********************** 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 : 1.327 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: 0.8438 (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: 0.6818 (tp30) cc_final: 0.6521 (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: 0.9395 (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: 0.8306 (p) REVERT: F 94 THR cc_start: 0.8456 (p) cc_final: 0.8184 (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: 0.8266 (tm-30) REVERT: F 145 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8687 (mmmm) REVERT: F 149 LYS cc_start: 0.9529 (mttt) cc_final: 0.9277 (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: 0.8037 (tp) cc_final: 0.7689 (pp) REVERT: G 186 SER cc_start: 0.8142 (t) cc_final: 0.7817 (p) REVERT: H 4 LEU cc_start: 0.7902 (mt) cc_final: 0.7648 (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: 0.8937 (m) cc_final: 0.8079 (p) outliers start: 54 outliers final: 33 residues processed: 326 average time/residue: 0.2959 time to fit residues: 130.6368 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 : 1.472 ------------------------------------------------------------------------------- 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: 10.0000 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 106 optimal weight: 0.0060 chunk 102 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN D 6 GLN 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 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.100765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.081523 restraints weight = 37835.058| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.57 r_work: 0.3466 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 13074 Z= 0.221 Angle : 0.713 12.096 17772 Z= 0.375 Chirality : 0.045 0.252 2006 Planarity : 0.005 0.046 2273 Dihedral : 5.285 20.644 1821 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.59 % Allowed : 12.11 % Favored : 83.30 % 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: 0.63 (0.20), residues: 1671 helix: -0.43 (0.58), residues: 64 sheet: 0.99 (0.18), residues: 767 loop : 0.02 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 96 HIS 0.008 0.001 HIS H 189 PHE 0.032 0.002 PHE G 152 TYR 0.023 0.002 TYR D 49 ARG 0.006 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 559) hydrogen bonds : angle 6.25835 ( 1398) covalent geometry : bond 0.00495 (13074) covalent geometry : angle 0.71294 (17772) *********************** 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 304 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 238 time to evaluate : 1.447 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: A 22 SER cc_start: 0.8527 (p) cc_final: 0.8248 (t) REVERT: A 28 PHE cc_start: 0.6637 (m-80) cc_final: 0.4158 (m-80) REVERT: A 35 MET cc_start: 0.9118 (mmp) cc_final: 0.8912 (mmp) REVERT: A 77 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8607 (ptpt) REVERT: A 108 TYR cc_start: 0.8318 (m-80) cc_final: 0.7980 (m-80) REVERT: C 78 ASN cc_start: 0.9300 (m-40) cc_final: 0.9069 (p0) REVERT: C 108 TYR cc_start: 0.8080 (m-80) cc_final: 0.7815 (m-80) REVERT: C 185 SER cc_start: 0.8942 (t) cc_final: 0.8646 (p) REVERT: D 89 GLN cc_start: 0.8849 (pp30) cc_final: 0.8446 (pp30) REVERT: D 122 ASP cc_start: 0.8683 (m-30) cc_final: 0.7855 (t0) REVERT: D 134 CYS cc_start: 0.8369 (t) cc_final: 0.8156 (t) REVERT: E 60 TYR cc_start: 0.8810 (m-80) cc_final: 0.8452 (m-80) REVERT: E 111 GLN cc_start: 0.9173 (tp40) cc_final: 0.8801 (mp10) REVERT: F 75 ILE cc_start: 0.8930 (mt) cc_final: 0.8663 (mt) REVERT: F 94 THR cc_start: 0.8502 (p) cc_final: 0.8140 (t) REVERT: F 143 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8762 (tm-30) REVERT: F 145 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8797 (mmmm) REVERT: F 149 LYS cc_start: 0.9606 (mttt) cc_final: 0.9299 (ttmm) REVERT: F 161 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8629 (tm-30) REVERT: G 40 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7903 (tm-30) REVERT: G 47 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.5644 (pp20) REVERT: G 147 LEU cc_start: 0.8297 (tp) cc_final: 0.7640 (pp) REVERT: H 149 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8145 (mmmt) outliers start: 66 outliers final: 48 residues processed: 279 average time/residue: 0.3013 time to fit residues: 116.7363 Evaluate side-chains 259 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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: 6.9990 chunk 148 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN C 177 GLN 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 G 177 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.101055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.081135 restraints weight = 37872.799| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 4.74 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13074 Z= 0.181 Angle : 0.654 9.777 17772 Z= 0.341 Chirality : 0.044 0.200 2006 Planarity : 0.005 0.049 2273 Dihedral : 5.067 19.536 1821 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.18 % Allowed : 13.36 % Favored : 82.46 % 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: 0.46 (0.20), residues: 1671 helix: -0.32 (0.60), residues: 64 sheet: 0.83 (0.18), residues: 759 loop : -0.05 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 148 HIS 0.008 0.001 HIS H 189 PHE 0.030 0.002 PHE G 152 TYR 0.017 0.002 TYR C 151 ARG 0.008 0.001 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 559) hydrogen bonds : angle 6.08464 ( 1398) covalent geometry : bond 0.00407 (13074) covalent geometry : angle 0.65429 (17772) *********************** 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 293 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 233 time to evaluate : 1.389 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 77 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8834 (mtpt) REVERT: A 81 TYR cc_start: 0.7887 (m-80) cc_final: 0.7522 (m-80) REVERT: B 70 ASP cc_start: 0.8878 (m-30) cc_final: 0.8573 (m-30) REVERT: C 77 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8558 (ptpt) REVERT: C 81 TYR cc_start: 0.8159 (m-80) cc_final: 0.7060 (m-10) REVERT: C 185 SER cc_start: 0.8886 (t) cc_final: 0.8570 (p) REVERT: D 70 ASP cc_start: 0.8255 (m-30) cc_final: 0.8019 (t0) REVERT: D 89 GLN cc_start: 0.8513 (pp30) cc_final: 0.8113 (pp30) REVERT: D 122 ASP cc_start: 0.8637 (m-30) cc_final: 0.7849 (t0) REVERT: E 60 TYR cc_start: 0.8470 (m-80) cc_final: 0.8096 (m-80) REVERT: E 111 GLN cc_start: 0.9126 (tp40) cc_final: 0.8717 (mp10) REVERT: E 177 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: F 75 ILE cc_start: 0.8912 (mt) cc_final: 0.8650 (mt) REVERT: F 94 THR cc_start: 0.8592 (p) cc_final: 0.8228 (t) REVERT: F 143 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8255 (tm-30) REVERT: F 145 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8768 (mmmm) REVERT: F 149 LYS cc_start: 0.9643 (mttt) cc_final: 0.9334 (ttmm) REVERT: F 161 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8446 (tm-30) REVERT: G 47 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5610 (pp20) REVERT: G 74 ASP cc_start: 0.7237 (t70) cc_final: 0.6874 (t70) REVERT: G 81 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: G 84 MET cc_start: 0.8620 (mtm) cc_final: 0.8334 (mpp) REVERT: G 128 PHE cc_start: 0.7919 (m-80) cc_final: 0.7718 (m-80) REVERT: G 147 LEU cc_start: 0.8308 (tp) cc_final: 0.7651 (pp) REVERT: G 212 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8795 (mmmm) REVERT: H 45 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7786 (ptm160) REVERT: H 149 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8000 (mmmt) outliers start: 60 outliers final: 41 residues processed: 270 average time/residue: 0.3054 time to fit residues: 115.4773 Evaluate side-chains 250 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 80 LEU Chi-restraints excluded: chain A residue 188 VAL 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 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 185 ASP 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 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 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: 3.9990 chunk 21 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 78 ASN D 37 GLN E 170 HIS 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 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.093892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.075305 restraints weight = 39462.602| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 4.32 r_work: 0.3420 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.128 13074 Z= 0.396 Angle : 0.830 8.854 17772 Z= 0.441 Chirality : 0.050 0.320 2006 Planarity : 0.006 0.049 2273 Dihedral : 5.961 26.712 1821 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.22 % Allowed : 13.85 % Favored : 80.93 % 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: -0.85 (0.58), residues: 64 sheet: 0.18 (0.18), residues: 787 loop : -0.53 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 96 HIS 0.007 0.002 HIS H 189 PHE 0.047 0.004 PHE E 152 TYR 0.025 0.003 TYR C 96 ARG 0.008 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.05174 ( 559) hydrogen bonds : angle 6.99337 ( 1398) covalent geometry : bond 0.00882 (13074) covalent geometry : angle 0.83014 (17772) *********************** 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 288 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 213 time to evaluate : 1.400 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 77 LYS cc_start: 0.9170 (mtmt) cc_final: 0.8749 (ptpt) REVERT: B 17 GLU cc_start: 0.7571 (tt0) cc_final: 0.7239 (tm-30) REVERT: B 70 ASP cc_start: 0.9016 (m-30) cc_final: 0.8739 (m-30) REVERT: C 28 PHE cc_start: 0.5377 (m-10) cc_final: 0.4627 (m-10) REVERT: C 71 ILE cc_start: 0.8914 (tt) cc_final: 0.8699 (tp) REVERT: C 81 TYR cc_start: 0.8394 (m-80) cc_final: 0.7408 (m-80) REVERT: C 108 TYR cc_start: 0.8053 (m-80) cc_final: 0.7724 (m-10) REVERT: D 70 ASP cc_start: 0.8526 (m-30) cc_final: 0.8221 (m-30) REVERT: D 71 PHE cc_start: 0.7959 (m-80) cc_final: 0.7743 (m-80) REVERT: D 89 GLN cc_start: 0.8678 (pp30) cc_final: 0.8275 (pp30) REVERT: D 122 ASP cc_start: 0.8732 (m-30) cc_final: 0.7969 (t0) REVERT: E 60 TYR cc_start: 0.8719 (m-80) cc_final: 0.8442 (m-80) REVERT: E 81 TYR cc_start: 0.8134 (m-80) cc_final: 0.7337 (m-80) REVERT: F 143 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8778 (tm-30) REVERT: F 145 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8957 (mmmm) REVERT: F 149 LYS cc_start: 0.9614 (mttt) cc_final: 0.9086 (mmmm) REVERT: G 35 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8432 (mmm) REVERT: G 47 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.6032 (pp20) REVERT: G 74 ASP cc_start: 0.7138 (t70) cc_final: 0.6695 (t70) REVERT: G 81 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: G 212 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8979 (mmmm) REVERT: H 31 ARG cc_start: 0.7074 (ttt-90) cc_final: 0.6541 (tmt-80) REVERT: H 33 LEU cc_start: 0.8123 (tt) cc_final: 0.7250 (tt) REVERT: H 149 LYS cc_start: 0.8687 (mmmm) cc_final: 0.8270 (mmmt) outliers start: 75 outliers final: 57 residues processed: 259 average time/residue: 0.2780 time to fit residues: 99.4585 Evaluate side-chains 253 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 54 TYR Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 74 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 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 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 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 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 13 VAL 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 204 VAL 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: 9.9990 chunk 121 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 111 GLN D 152 ASN E 111 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 198 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.097758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.078553 restraints weight = 38833.403| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 4.46 r_work: 0.3426 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13074 Z= 0.159 Angle : 0.661 9.372 17772 Z= 0.343 Chirality : 0.044 0.199 2006 Planarity : 0.005 0.050 2273 Dihedral : 5.160 21.788 1821 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.90 % Allowed : 15.94 % Favored : 80.17 % 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: -0.13 (0.20), residues: 1671 helix: -0.47 (0.61), residues: 64 sheet: 0.30 (0.18), residues: 770 loop : -0.32 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 148 HIS 0.006 0.001 HIS H 189 PHE 0.028 0.002 PHE G 152 TYR 0.016 0.002 TYR E 96 ARG 0.005 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 559) hydrogen bonds : angle 6.26611 ( 1398) covalent geometry : bond 0.00358 (13074) covalent geometry : angle 0.66122 (17772) *********************** 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 275 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 1.509 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 28 PHE cc_start: 0.8197 (p90) cc_final: 0.7983 (p90) REVERT: A 77 LYS cc_start: 0.9129 (mtmt) cc_final: 0.8686 (ptpt) REVERT: B 17 GLU cc_start: 0.7700 (tt0) cc_final: 0.7353 (tm-30) REVERT: B 70 ASP cc_start: 0.9006 (m-30) cc_final: 0.8803 (m-30) REVERT: B 147 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7600 (mt0) REVERT: C 84 MET cc_start: 0.8857 (mpp) cc_final: 0.8656 (mpp) REVERT: C 111 GLN cc_start: 0.9001 (tp40) cc_final: 0.7631 (mp10) REVERT: D 70 ASP cc_start: 0.8556 (m-30) cc_final: 0.8195 (m-30) REVERT: D 71 PHE cc_start: 0.7644 (m-80) cc_final: 0.7435 (m-80) REVERT: D 89 GLN cc_start: 0.8725 (pp30) cc_final: 0.8310 (pp30) REVERT: D 122 ASP cc_start: 0.8717 (m-30) cc_final: 0.7948 (t0) REVERT: E 60 TYR cc_start: 0.8822 (m-80) cc_final: 0.8618 (m-80) REVERT: E 81 TYR cc_start: 0.8137 (m-80) cc_final: 0.7472 (m-80) REVERT: E 90 GLU cc_start: 0.7717 (pp20) cc_final: 0.7472 (pp20) REVERT: E 111 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8841 (mp10) REVERT: E 212 LYS cc_start: 0.8137 (tppt) cc_final: 0.7932 (tppt) REVERT: F 102 THR cc_start: 0.7471 (OUTLIER) cc_final: 0.7033 (t) REVERT: F 143 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8649 (tm-30) REVERT: F 145 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8877 (mmmm) REVERT: F 149 LYS cc_start: 0.9571 (mttt) cc_final: 0.9288 (ttmm) REVERT: G 35 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8413 (mmm) REVERT: G 74 ASP cc_start: 0.7332 (t70) cc_final: 0.6858 (t70) REVERT: G 81 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6341 (m-80) REVERT: G 212 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8949 (mmmm) REVERT: G 216 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7678 (tmtt) REVERT: H 31 ARG cc_start: 0.6925 (ttt-90) cc_final: 0.6204 (tmt-80) REVERT: H 33 LEU cc_start: 0.8069 (tt) cc_final: 0.7254 (tt) REVERT: H 45 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7787 (ptm160) REVERT: H 149 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8308 (mmmt) REVERT: H 169 LYS cc_start: 0.7546 (mttt) cc_final: 0.7227 (pttp) REVERT: H 174 SER cc_start: 0.9055 (OUTLIER) cc_final: 0.8505 (p) outliers start: 56 outliers final: 38 residues processed: 257 average time/residue: 0.2866 time to fit residues: 102.1449 Evaluate side-chains 250 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 74 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 48 ILE Chi-restraints excluded: chain B residue 147 GLN 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 104 GLN Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 88 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 84 MET Chi-restraints excluded: chain E residue 111 GLN Chi-restraints excluded: chain E residue 147 LEU 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 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 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 174 SER 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: 10.0000 chunk 67 optimal weight: 4.9990 chunk 128 optimal weight: 0.1980 chunk 65 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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 ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** 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 = 0.3954 r_free = 0.3954 target = 0.095846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.076729 restraints weight = 39070.110| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 4.46 r_work: 0.3386 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.6444 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= 0.227 Angle : 0.697 9.025 17772 Z= 0.364 Chirality : 0.045 0.250 2006 Planarity : 0.005 0.053 2273 Dihedral : 5.249 22.085 1821 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.52 % Allowed : 16.08 % Favored : 79.40 % 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: -0.24 (0.20), residues: 1671 helix: -0.35 (0.62), residues: 64 sheet: 0.19 (0.18), residues: 780 loop : -0.39 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 148 HIS 0.006 0.001 HIS H 189 PHE 0.032 0.002 PHE G 152 TYR 0.019 0.002 TYR E 96 ARG 0.004 0.001 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.04192 ( 559) hydrogen bonds : angle 6.32767 ( 1398) covalent geometry : bond 0.00512 (13074) covalent geometry : angle 0.69699 (17772) *********************** 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 267 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 202 time to evaluate : 1.500 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 77 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8726 (ptpt) REVERT: B 17 GLU cc_start: 0.7717 (tt0) cc_final: 0.7305 (tm-30) REVERT: B 70 ASP cc_start: 0.9067 (m-30) cc_final: 0.8833 (m-30) REVERT: B 147 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: C 77 LYS cc_start: 0.8834 (ptpp) cc_final: 0.8544 (pttp) REVERT: C 81 TYR cc_start: 0.8409 (m-80) cc_final: 0.8074 (m-80) REVERT: C 105 THR cc_start: 0.7276 (OUTLIER) cc_final: 0.6813 (p) REVERT: D 18 ARG cc_start: 0.8930 (tpp80) cc_final: 0.8668 (mmm-85) REVERT: D 70 ASP cc_start: 0.8635 (m-30) cc_final: 0.8354 (m-30) REVERT: D 89 GLN cc_start: 0.8735 (pp30) cc_final: 0.8305 (pp30) REVERT: D 122 ASP cc_start: 0.8776 (m-30) cc_final: 0.7988 (t0) REVERT: E 60 TYR cc_start: 0.8796 (m-80) cc_final: 0.8578 (m-80) REVERT: E 81 TYR cc_start: 0.8100 (m-80) cc_final: 0.7505 (m-80) REVERT: E 111 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8929 (mp10) REVERT: F 143 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8687 (tm-30) REVERT: F 145 LYS cc_start: 0.9157 (mmmt) cc_final: 0.8864 (mmmm) REVERT: F 149 LYS cc_start: 0.9575 (mttt) cc_final: 0.9273 (ttmm) REVERT: G 35 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8574 (mmm) REVERT: G 74 ASP cc_start: 0.7179 (t70) cc_final: 0.6683 (t70) REVERT: G 81 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: G 154 GLU cc_start: 0.8062 (tt0) cc_final: 0.7823 (mp0) REVERT: G 216 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7807 (tmtt) REVERT: H 31 ARG cc_start: 0.6982 (ttt-90) cc_final: 0.6443 (tmt-80) REVERT: H 149 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8316 (mmmt) outliers start: 65 outliers final: 53 residues processed: 242 average time/residue: 0.2765 time to fit residues: 92.8771 Evaluate side-chains 250 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 74 ASP 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 217 VAL 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 147 GLN Chi-restraints excluded: chain B residue 156 SER 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 88 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 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 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 81 TYR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 204 VAL 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 174 SER 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 127 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 0.0980 chunk 161 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 104 GLN E 111 GLN E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.098929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.079798 restraints weight = 38758.131| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 4.49 r_work: 0.3427 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.6580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13074 Z= 0.164 Angle : 0.677 9.258 17772 Z= 0.349 Chirality : 0.044 0.205 2006 Planarity : 0.005 0.055 2273 Dihedral : 5.007 20.733 1821 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.83 % Allowed : 17.05 % 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 (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: -0.23 (0.20), residues: 1671 helix: -0.74 (0.58), residues: 64 sheet: 0.22 (0.18), residues: 779 loop : -0.36 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 148 HIS 0.006 0.001 HIS H 189 PHE 0.029 0.002 PHE G 152 TYR 0.017 0.002 TYR E 96 ARG 0.008 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 559) hydrogen bonds : angle 6.18189 ( 1398) covalent geometry : bond 0.00373 (13074) covalent geometry : angle 0.67663 (17772) *********************** 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: 55 poor density : 201 time to evaluate : 1.364 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: B 17 GLU cc_start: 0.7735 (tt0) cc_final: 0.7347 (tm-30) REVERT: B 147 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: C 77 LYS cc_start: 0.8854 (ptpp) cc_final: 0.8581 (pttp) REVERT: C 81 TYR cc_start: 0.8449 (m-80) cc_final: 0.8056 (m-80) REVERT: C 99 ARG cc_start: 0.7286 (ttp-170) cc_final: 0.6852 (ttp-170) REVERT: C 105 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.7131 (p) REVERT: C 108 TYR cc_start: 0.8074 (m-80) cc_final: 0.7507 (m-80) REVERT: D 89 GLN cc_start: 0.8774 (pp30) cc_final: 0.8357 (pp30) REVERT: D 122 ASP cc_start: 0.8770 (m-30) cc_final: 0.8056 (t0) REVERT: E 81 TYR cc_start: 0.8038 (m-80) cc_final: 0.7414 (m-80) REVERT: E 205 ASN cc_start: 0.5301 (OUTLIER) cc_final: 0.4941 (t0) REVERT: F 102 THR cc_start: 0.7493 (OUTLIER) cc_final: 0.7039 (t) REVERT: F 143 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8650 (tm-30) REVERT: F 145 LYS cc_start: 0.9166 (mmmt) cc_final: 0.8883 (mmmm) REVERT: F 149 LYS cc_start: 0.9545 (mttt) cc_final: 0.9080 (mmmm) REVERT: G 74 ASP cc_start: 0.7257 (t70) cc_final: 0.6861 (t70) REVERT: G 81 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: G 212 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8690 (mmmt) REVERT: G 216 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7869 (tmtt) REVERT: H 31 ARG cc_start: 0.6967 (ttt-90) cc_final: 0.6383 (tmt-80) REVERT: H 123 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8293 (tp30) REVERT: H 149 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8353 (mmmt) REVERT: H 169 LYS cc_start: 0.7505 (mttt) cc_final: 0.7247 (pttp) outliers start: 55 outliers final: 43 residues processed: 240 average time/residue: 0.2885 time to fit residues: 95.7485 Evaluate side-chains 244 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 74 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 48 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 156 SER 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 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 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 147 LEU 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 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 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 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 174 SER 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 161 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 147 optimal weight: 0.0470 chunk 120 optimal weight: 0.9980 chunk 149 optimal weight: 0.0060 chunk 119 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- 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 4 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** G 205 ASN ** 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 = 0.4049 r_free = 0.4049 target = 0.102224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.082873 restraints weight = 38023.179| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 4.48 r_work: 0.3481 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13074 Z= 0.120 Angle : 0.665 9.273 17772 Z= 0.338 Chirality : 0.044 0.173 2006 Planarity : 0.005 0.054 2273 Dihedral : 4.678 18.248 1821 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.06 % Allowed : 18.30 % Favored : 78.64 % 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 (0.21), residues: 1671 helix: -0.69 (0.60), residues: 63 sheet: 0.30 (0.18), residues: 794 loop : -0.26 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 148 HIS 0.004 0.001 HIS H 189 PHE 0.021 0.002 PHE G 152 TYR 0.017 0.001 TYR H 186 ARG 0.009 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 559) hydrogen bonds : angle 5.89525 ( 1398) covalent geometry : bond 0.00273 (13074) covalent geometry : angle 0.66529 (17772) *********************** 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 261 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 217 time to evaluate : 1.383 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 77 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8696 (ptpt) REVERT: B 17 GLU cc_start: 0.7860 (tt0) cc_final: 0.7468 (tm-30) REVERT: B 70 ASP cc_start: 0.8708 (m-30) cc_final: 0.8388 (t0) REVERT: B 147 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: C 77 LYS cc_start: 0.8779 (ptpp) cc_final: 0.8501 (pttm) REVERT: C 81 TYR cc_start: 0.8490 (m-80) cc_final: 0.7861 (m-10) REVERT: C 99 ARG cc_start: 0.7023 (ttp-170) cc_final: 0.6637 (ttp-170) REVERT: C 106 PHE cc_start: 0.7838 (m-10) cc_final: 0.7596 (m-10) REVERT: C 108 TYR cc_start: 0.8118 (m-80) cc_final: 0.7600 (m-80) REVERT: C 111 GLN cc_start: 0.8362 (tp40) cc_final: 0.7590 (pp30) REVERT: D 70 ASP cc_start: 0.8464 (m-30) cc_final: 0.8215 (t0) REVERT: D 89 GLN cc_start: 0.8768 (pp30) cc_final: 0.8432 (pp30) REVERT: D 122 ASP cc_start: 0.8705 (m-30) cc_final: 0.7876 (t0) REVERT: E 81 TYR cc_start: 0.7937 (m-80) cc_final: 0.7363 (m-80) REVERT: E 105 THR cc_start: 0.8317 (p) cc_final: 0.8048 (p) REVERT: F 102 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.6973 (t) REVERT: F 126 LYS cc_start: 0.9284 (mmmt) cc_final: 0.8831 (pttp) REVERT: F 132 VAL cc_start: 0.7411 (t) cc_final: 0.7193 (m) REVERT: F 143 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8484 (tm-30) REVERT: F 145 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8870 (mmmm) REVERT: F 149 LYS cc_start: 0.9510 (mttt) cc_final: 0.9049 (mmmm) REVERT: G 20 ARG cc_start: 0.8874 (ttt90) cc_final: 0.8604 (tpp80) REVERT: G 74 ASP cc_start: 0.7270 (t70) cc_final: 0.6835 (t70) REVERT: G 81 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: G 216 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7943 (tmtt) REVERT: H 31 ARG cc_start: 0.6853 (ttt-90) cc_final: 0.6304 (tmt-80) REVERT: H 33 LEU cc_start: 0.8047 (tt) cc_final: 0.7313 (tt) REVERT: H 70 ASP cc_start: 0.7982 (m-30) cc_final: 0.7774 (t0) REVERT: H 149 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8219 (mmmt) REVERT: H 169 LYS cc_start: 0.7606 (mttt) cc_final: 0.7299 (pttp) REVERT: H 174 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8538 (p) outliers start: 44 outliers final: 31 residues processed: 250 average time/residue: 0.2839 time to fit residues: 97.6133 Evaluate side-chains 238 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 74 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain C residue 60 TYR 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 E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE 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 195 LEU Chi-restraints excluded: chain E residue 217 VAL 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 81 TYR 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 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 174 SER 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 131 optimal weight: 0.3980 chunk 142 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 18 optimal weight: 0.1980 chunk 129 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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** B 166 GLN D 138 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN H 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.100721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.081365 restraints weight = 38282.837| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 4.48 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: 0.7487 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13074 Z= 0.150 Angle : 0.680 9.355 17772 Z= 0.347 Chirality : 0.044 0.325 2006 Planarity : 0.005 0.051 2273 Dihedral : 4.700 19.335 1821 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.85 % Allowed : 18.44 % Favored : 78.71 % 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: -0.08 (0.21), residues: 1671 helix: -0.81 (0.58), residues: 64 sheet: 0.34 (0.18), residues: 776 loop : -0.27 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 148 HIS 0.004 0.001 HIS H 189 PHE 0.025 0.002 PHE G 152 TYR 0.020 0.002 TYR A 182 ARG 0.009 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 559) hydrogen bonds : angle 5.89130 ( 1398) covalent geometry : bond 0.00347 (13074) covalent geometry : angle 0.67960 (17772) ********************** 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 249 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 1.351 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: A 77 LYS cc_start: 0.9145 (mtmt) cc_final: 0.8696 (ptpt) REVERT: A 101 ARG cc_start: 0.5214 (ttt90) cc_final: 0.4620 (ttt90) REVERT: B 17 GLU cc_start: 0.7981 (tt0) cc_final: 0.7543 (tm-30) REVERT: B 70 ASP cc_start: 0.8745 (m-30) cc_final: 0.8415 (t0) REVERT: B 147 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: C 81 TYR cc_start: 0.8459 (m-80) cc_final: 0.7985 (m-10) REVERT: C 99 ARG cc_start: 0.7158 (ttp-170) cc_final: 0.6308 (ttp-170) REVERT: C 106 PHE cc_start: 0.7877 (m-10) cc_final: 0.7595 (m-10) REVERT: C 108 TYR cc_start: 0.8110 (m-80) cc_final: 0.7516 (m-80) REVERT: D 70 ASP cc_start: 0.8425 (m-30) cc_final: 0.8146 (t0) REVERT: D 89 GLN cc_start: 0.8745 (pp30) cc_final: 0.8436 (pp30) REVERT: D 122 ASP cc_start: 0.8724 (m-30) cc_final: 0.7990 (t0) REVERT: E 81 TYR cc_start: 0.7956 (m-80) cc_final: 0.7399 (m-80) REVERT: F 102 THR cc_start: 0.7429 (OUTLIER) cc_final: 0.6983 (t) REVERT: F 126 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8821 (pttp) REVERT: F 132 VAL cc_start: 0.7399 (t) cc_final: 0.7154 (m) REVERT: F 143 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8508 (tm-30) REVERT: F 145 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8905 (mmmm) REVERT: F 149 LYS cc_start: 0.9519 (mttt) cc_final: 0.8970 (mmmm) REVERT: F 195 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7085 (mp0) REVERT: G 20 ARG cc_start: 0.8897 (ttt90) cc_final: 0.8620 (tpp80) REVERT: G 74 ASP cc_start: 0.7191 (t70) cc_final: 0.6771 (t70) REVERT: G 81 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6985 (m-80) REVERT: G 207 LYS cc_start: 0.8907 (tppt) cc_final: 0.8514 (mmtm) REVERT: G 216 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8071 (tmtt) REVERT: H 24 ARG cc_start: 0.8330 (mmp80) cc_final: 0.7691 (mmp80) REVERT: H 31 ARG cc_start: 0.6955 (ttt-90) cc_final: 0.6399 (tmt-80) REVERT: H 33 LEU cc_start: 0.7974 (tt) cc_final: 0.7222 (tt) REVERT: H 70 ASP cc_start: 0.8073 (m-30) cc_final: 0.7868 (t0) REVERT: H 123 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8290 (tp30) REVERT: H 169 LYS cc_start: 0.7571 (mttt) cc_final: 0.7295 (pttp) outliers start: 41 outliers final: 34 residues processed: 235 average time/residue: 0.2943 time to fit residues: 97.2571 Evaluate side-chains 238 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 74 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 123 GLU Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 60 TYR 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 E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE 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 195 LEU 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 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 162 SER Chi-restraints excluded: chain G residue 177 GLN Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 213 VAL 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 121 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** G 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.100292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.080973 restraints weight = 38514.560| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 4.47 r_work: 0.3444 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.282 13074 Z= 0.263 Angle : 0.896 59.193 17772 Z= 0.507 Chirality : 0.046 0.343 2006 Planarity : 0.005 0.071 2273 Dihedral : 4.747 28.065 1821 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 2.71 % Allowed : 19.14 % Favored : 78.15 % 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: -0.10 (0.21), residues: 1671 helix: -0.81 (0.58), residues: 64 sheet: 0.33 (0.18), residues: 776 loop : -0.28 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 148 HIS 0.004 0.001 HIS H 189 PHE 0.025 0.002 PHE G 152 TYR 0.048 0.002 TYR B 173 ARG 0.109 0.001 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 559) hydrogen bonds : angle 5.89575 ( 1398) covalent geometry : bond 0.00657 (13074) covalent geometry : angle 0.89593 (17772) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7128.21 seconds wall clock time: 123 minutes 47.60 seconds (7427.60 seconds total)