Starting phenix.real_space_refine on Sun Nov 17 04:23:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2e_17362/11_2024/8p2e_17362.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2e_17362/11_2024/8p2e_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2e_17362/11_2024/8p2e_17362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2e_17362/11_2024/8p2e_17362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2e_17362/11_2024/8p2e_17362.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p2e_17362/11_2024/8p2e_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.37, per 1000 atoms: 0.65 Number of scatterers: 12786 At special positions: 0 Unit cell: (90.688, 131.456, 130.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2551 8.00 N 2180 7.00 C 8015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.9 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: 2.32 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: 4.89 Time building geometry restraints manager: 3.58 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 33.240 Find NCS groups from input model: 0.640 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.128 13074 Z= 1.174 Angle : 1.788 12.944 17772 Z= 1.199 Chirality : 0.092 0.421 2006 Planarity : 0.012 0.366 2273 Dihedral : 10.288 88.503 4666 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.92 % Favored : 97.73 % Rotamer: Outliers : 0.14 % Allowed : 0.97 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1671 helix: -0.44 (0.59), residues: 64 sheet: 1.23 (0.18), residues: 769 loop : 0.64 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.009 TRP F 35 HIS 0.012 0.003 HIS E 170 PHE 0.033 0.006 PHE B 83 TYR 0.067 0.009 TYR E 182 ARG 0.006 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 1.410 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: 0.3339 time to fit residues: 208.9793 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 : 1.549 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13074 Z= 0.261 Angle : 0.740 9.670 17772 Z= 0.394 Chirality : 0.046 0.210 2006 Planarity : 0.005 0.042 2273 Dihedral : 5.420 24.877 1821 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.76 % Allowed : 10.51 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.20), residues: 1671 helix: -0.37 (0.54), residues: 62 sheet: 1.24 (0.18), residues: 755 loop : 0.30 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 96 HIS 0.005 0.001 HIS A 206 PHE 0.033 0.002 PHE G 152 TYR 0.039 0.002 TYR D 49 ARG 0.007 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 294 time to evaluate : 1.507 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 28 PHE cc_start: 0.5641 (m-80) cc_final: 0.5235 (m-80) REVERT: A 77 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8491 (ptpt) REVERT: A 81 TYR cc_start: 0.7991 (m-80) cc_final: 0.7643 (m-80) REVERT: A 90 GLU cc_start: 0.8411 (pp20) cc_final: 0.8198 (pp20) REVERT: C 77 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8755 (mtmt) REVERT: C 78 ASN cc_start: 0.9317 (m-40) cc_final: 0.8900 (p0) REVERT: C 81 TYR cc_start: 0.7743 (m-80) cc_final: 0.6838 (m-10) REVERT: D 122 ASP cc_start: 0.8311 (m-30) cc_final: 0.7817 (t0) REVERT: E 60 TYR cc_start: 0.8485 (m-80) cc_final: 0.8231 (m-80) REVERT: F 94 THR cc_start: 0.8338 (p) cc_final: 0.8047 (t) REVERT: F 102 THR cc_start: 0.7289 (OUTLIER) cc_final: 0.7062 (t) REVERT: G 128 PHE cc_start: 0.7488 (m-80) cc_final: 0.7117 (m-80) REVERT: H 174 SER cc_start: 0.8705 (m) cc_final: 0.8065 (p) outliers start: 54 outliers final: 33 residues processed: 326 average time/residue: 0.3106 time to fit residues: 137.0755 Evaluate side-chains 251 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 185 ASP 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 82 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 123 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN B 6 GLN C 177 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13074 Z= 0.349 Angle : 0.733 12.748 17772 Z= 0.384 Chirality : 0.046 0.261 2006 Planarity : 0.005 0.045 2273 Dihedral : 5.365 21.488 1821 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.66 % Allowed : 12.39 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.20), residues: 1671 helix: -0.36 (0.58), residues: 64 sheet: 0.97 (0.18), residues: 772 loop : 0.01 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 96 HIS 0.009 0.002 HIS H 189 PHE 0.034 0.002 PHE G 152 TYR 0.023 0.002 TYR D 49 ARG 0.007 0.001 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3342 Ramachandran restraints generated. 1671 Oldfield, 0 Emsley, 1671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 225 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 PHE cc_start: 0.5889 (m-80) cc_final: 0.5230 (m-80) REVERT: C 78 ASN cc_start: 0.9283 (m-40) cc_final: 0.9046 (p0) REVERT: D 70 ASP cc_start: 0.8175 (m-30) cc_final: 0.7957 (m-30) REVERT: D 89 GLN cc_start: 0.8345 (pp30) cc_final: 0.8085 (pp30) REVERT: D 122 ASP cc_start: 0.8378 (m-30) cc_final: 0.7906 (t0) REVERT: E 60 TYR cc_start: 0.8466 (m-80) cc_final: 0.8219 (m-80) REVERT: F 94 THR cc_start: 0.8451 (p) cc_final: 0.8091 (t) REVERT: G 74 ASP cc_start: 0.8180 (t0) cc_final: 0.7930 (t70) REVERT: G 81 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.6752 (m-80) outliers start: 67 outliers final: 53 residues processed: 268 average time/residue: 0.2864 time to fit residues: 106.6898 Evaluate side-chains 257 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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 65 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 35 MET Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 81 TYR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain H residue 39 LYS Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.0050 chunk 16 optimal weight: 0.0980 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 ASN H 124 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13074 Z= 0.189 Angle : 0.642 9.446 17772 Z= 0.329 Chirality : 0.043 0.188 2006 Planarity : 0.004 0.049 2273 Dihedral : 4.916 18.217 1821 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.27 % Allowed : 13.92 % Favored : 82.81 % 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: 0.59 (0.20), residues: 1671 helix: -0.16 (0.60), residues: 64 sheet: 0.89 (0.18), residues: 769 loop : 0.05 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 148 HIS 0.008 0.001 HIS H 189 PHE 0.024 0.002 PHE G 152 TYR 0.017 0.002 TYR A 54 ARG 0.005 0.001 ARG B 18 *********************** 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 287 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 1.494 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 28 PHE cc_start: 0.5701 (m-80) cc_final: 0.4583 (m-80) REVERT: A 90 GLU cc_start: 0.8370 (pp20) cc_final: 0.7973 (pp20) REVERT: A 107 ASP cc_start: 0.8195 (p0) cc_final: 0.7629 (p0) REVERT: C 77 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8392 (ptpt) REVERT: C 81 TYR cc_start: 0.7741 (m-80) cc_final: 0.6988 (m-10) REVERT: D 89 GLN cc_start: 0.8314 (pp30) cc_final: 0.8061 (pp30) REVERT: D 122 ASP cc_start: 0.8371 (m-30) cc_final: 0.7986 (t0) REVERT: E 108 TYR cc_start: 0.7672 (m-80) cc_final: 0.7453 (m-80) REVERT: F 94 THR cc_start: 0.8441 (p) cc_final: 0.8080 (t) REVERT: F 102 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6878 (t) REVERT: H 24 ARG cc_start: 0.8607 (mmp80) cc_final: 0.8266 (mmp80) REVERT: H 174 SER cc_start: 0.8857 (t) cc_final: 0.8452 (p) outliers start: 47 outliers final: 33 residues processed: 267 average time/residue: 0.2866 time to fit residues: 106.0979 Evaluate side-chains 248 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 58 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL 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 125 LEU Chi-restraints excluded: chain D residue 135 LEU 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 84 MET Chi-restraints excluded: chain E residue 130 LEU 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 170 ASP 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 80 LEU 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 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 135 optimal weight: 0.0470 chunk 109 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 142 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN C 177 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 GLN G 177 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.5658 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= 0.209 Angle : 0.635 12.133 17772 Z= 0.326 Chirality : 0.043 0.187 2006 Planarity : 0.005 0.048 2273 Dihedral : 4.838 17.976 1821 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.48 % Allowed : 15.03 % Favored : 81.49 % 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: 0.52 (0.21), residues: 1671 helix: -0.09 (0.62), residues: 64 sheet: 0.76 (0.18), residues: 780 loop : 0.07 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 148 HIS 0.007 0.001 HIS H 189 PHE 0.024 0.002 PHE G 152 TYR 0.017 0.002 TYR A 54 ARG 0.013 0.001 ARG D 18 *********************** 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 278 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 1.248 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: A 77 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8433 (pttt) REVERT: B 70 ASP cc_start: 0.8035 (m-30) cc_final: 0.7697 (t0) REVERT: B 75 ILE cc_start: 0.7193 (tp) cc_final: 0.6988 (tp) REVERT: C 77 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8667 (ptpp) REVERT: C 81 TYR cc_start: 0.7755 (m-80) cc_final: 0.7338 (m-80) REVERT: D 89 GLN cc_start: 0.8310 (pp30) cc_final: 0.8074 (pp30) REVERT: D 122 ASP cc_start: 0.8372 (m-30) cc_final: 0.7946 (t0) REVERT: E 81 TYR cc_start: 0.7851 (m-80) cc_final: 0.7624 (m-80) REVERT: F 94 THR cc_start: 0.8468 (p) cc_final: 0.8048 (t) REVERT: G 74 ASP cc_start: 0.8129 (t70) cc_final: 0.7657 (t70) REVERT: G 81 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6044 (m-80) REVERT: H 174 SER cc_start: 0.8864 (t) cc_final: 0.8447 (p) outliers start: 50 outliers final: 37 residues processed: 259 average time/residue: 0.2842 time to fit residues: 102.4137 Evaluate side-chains 243 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL 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 146 CYS Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 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 189 THR 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 G residue 23 CYS 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 135 LEU Chi-restraints excluded: chain H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 0.0060 chunk 39 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 83 optimal weight: 0.0270 overall best weight: 2.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13074 Z= 0.334 Angle : 0.685 12.060 17772 Z= 0.357 Chirality : 0.044 0.187 2006 Planarity : 0.005 0.052 2273 Dihedral : 5.064 19.850 1821 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.31 % Allowed : 14.82 % Favored : 80.86 % 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: 0.25 (0.21), residues: 1671 helix: -0.02 (0.61), residues: 64 sheet: 0.55 (0.18), residues: 781 loop : -0.09 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 148 HIS 0.006 0.001 HIS H 189 PHE 0.032 0.002 PHE E 152 TYR 0.016 0.002 TYR C 96 ARG 0.006 0.001 ARG B 18 *********************** 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 276 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 214 time to evaluate : 1.511 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: 0.8771 (ptmt) cc_final: 0.8392 (pttt) REVERT: A 90 GLU cc_start: 0.8379 (pp20) cc_final: 0.7912 (pp20) REVERT: B 143 GLU cc_start: 0.8770 (tp30) cc_final: 0.8469 (tp30) REVERT: C 108 TYR cc_start: 0.7948 (m-80) cc_final: 0.7600 (m-80) REVERT: C 111 GLN cc_start: 0.7859 (pt0) cc_final: 0.7294 (mp10) REVERT: D 89 GLN cc_start: 0.8348 (pp30) cc_final: 0.8046 (pp30) REVERT: D 122 ASP cc_start: 0.8444 (m-30) cc_final: 0.8018 (t0) REVERT: E 81 TYR cc_start: 0.7819 (m-80) cc_final: 0.7618 (m-80) REVERT: F 94 THR cc_start: 0.8589 (p) cc_final: 0.8148 (t) REVERT: G 81 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6234 (m-80) REVERT: H 126 LYS cc_start: 0.9478 (ptpt) cc_final: 0.9190 (ptpt) outliers start: 62 outliers final: 47 residues processed: 253 average time/residue: 0.2846 time to fit residues: 100.5197 Evaluate side-chains 243 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 38 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 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 217 VAL 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 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 84 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 170 ASP 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 80 LEU Chi-restraints excluded: chain G residue 81 TYR Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 214 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 133 optimal weight: 0.0870 chunk 88 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 ASN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.6192 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= 0.183 Angle : 0.657 12.000 17772 Z= 0.333 Chirality : 0.043 0.210 2006 Planarity : 0.005 0.049 2273 Dihedral : 4.737 17.867 1821 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.85 % Allowed : 17.75 % 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 (0.21), residues: 1671 helix: -0.46 (0.57), residues: 64 sheet: 0.50 (0.18), residues: 785 loop : -0.01 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 148 HIS 0.006 0.001 HIS H 189 PHE 0.023 0.002 PHE G 152 TYR 0.016 0.001 TYR A 54 ARG 0.007 0.001 ARG B 18 *********************** 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 264 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8644 (ptmt) cc_final: 0.8241 (pttt) REVERT: C 77 LYS cc_start: 0.8865 (ptpp) cc_final: 0.8610 (pttp) REVERT: C 108 TYR cc_start: 0.7867 (m-80) cc_final: 0.7583 (m-80) REVERT: C 111 GLN cc_start: 0.7756 (pt0) cc_final: 0.7213 (mp10) REVERT: D 70 ASP cc_start: 0.8282 (m-30) cc_final: 0.8004 (t0) REVERT: D 89 GLN cc_start: 0.8346 (pp30) cc_final: 0.8116 (pp30) REVERT: D 122 ASP cc_start: 0.8404 (m-30) cc_final: 0.7971 (t0) REVERT: E 105 THR cc_start: 0.7935 (p) cc_final: 0.7708 (p) REVERT: E 177 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7904 (mp10) REVERT: F 94 THR cc_start: 0.8565 (p) cc_final: 0.8124 (t) REVERT: F 102 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6856 (t) REVERT: F 126 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8819 (pttp) REVERT: G 80 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8575 (tp) REVERT: G 81 TYR cc_start: 0.7482 (OUTLIER) cc_final: 0.6251 (m-80) REVERT: G 128 PHE cc_start: 0.7714 (m-80) cc_final: 0.7366 (m-80) REVERT: H 169 LYS cc_start: 0.7514 (mttt) cc_final: 0.7312 (pttp) outliers start: 41 outliers final: 32 residues processed: 251 average time/residue: 0.2867 time to fit residues: 100.5685 Evaluate side-chains 245 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 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 102 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain G residue 23 CYS 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 H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 0.0870 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 overall best weight: 2.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13074 Z= 0.314 Angle : 0.706 12.601 17772 Z= 0.362 Chirality : 0.045 0.218 2006 Planarity : 0.005 0.055 2273 Dihedral : 4.969 19.486 1821 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.76 % Allowed : 16.98 % Favored : 79.26 % 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: -0.68 (0.59), residues: 64 sheet: 0.45 (0.18), residues: 763 loop : -0.12 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 148 HIS 0.006 0.001 HIS H 189 PHE 0.029 0.002 PHE G 152 TYR 0.019 0.002 TYR A 182 ARG 0.018 0.001 ARG B 24 *********************** 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 268 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 1.706 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: 0.8709 (ptmt) cc_final: 0.8355 (pttt) REVERT: A 90 GLU cc_start: 0.8393 (pp20) cc_final: 0.7897 (pp20) REVERT: B 143 GLU cc_start: 0.8698 (tp30) cc_final: 0.8463 (tp30) REVERT: C 77 LYS cc_start: 0.8857 (ptpp) cc_final: 0.8578 (pttp) REVERT: C 81 TYR cc_start: 0.8057 (m-80) cc_final: 0.7796 (m-80) REVERT: C 108 TYR cc_start: 0.7948 (m-80) cc_final: 0.7618 (m-80) REVERT: C 111 GLN cc_start: 0.7923 (pt0) cc_final: 0.7269 (mp10) REVERT: D 70 ASP cc_start: 0.8429 (m-30) cc_final: 0.8131 (t0) REVERT: D 89 GLN cc_start: 0.8376 (pp30) cc_final: 0.8106 (pp30) REVERT: D 122 ASP cc_start: 0.8410 (m-30) cc_final: 0.8040 (t0) REVERT: F 94 THR cc_start: 0.8654 (p) cc_final: 0.8178 (t) REVERT: G 81 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: H 70 ASP cc_start: 0.7186 (m-30) cc_final: 0.6974 (t0) REVERT: H 125 LEU cc_start: 0.9154 (pp) cc_final: 0.8795 (mp) REVERT: H 169 LYS cc_start: 0.7446 (mttt) cc_final: 0.7233 (pttp) outliers start: 54 outliers final: 48 residues processed: 249 average time/residue: 0.2869 time to fit residues: 99.1695 Evaluate side-chains 253 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 38 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 188 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain 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 54 TYR Chi-restraints excluded: chain C residue 60 TYR 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 167 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 150 VAL 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 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 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 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 143 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 115 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN H 124 GLN ** H 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.6541 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= 0.195 Angle : 0.704 12.998 17772 Z= 0.351 Chirality : 0.043 0.188 2006 Planarity : 0.005 0.065 2273 Dihedral : 4.735 17.704 1821 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.71 % Allowed : 18.37 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.15 (0.21), residues: 1671 helix: -0.75 (0.59), residues: 64 sheet: 0.41 (0.18), residues: 794 loop : -0.03 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 148 HIS 0.005 0.001 HIS H 189 PHE 0.024 0.002 PHE G 128 TYR 0.017 0.001 TYR A 54 ARG 0.011 0.001 ARG B 24 *********************** 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 249 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 1.481 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: A 77 LYS cc_start: 0.8612 (ptmt) cc_final: 0.8254 (pttt) REVERT: C 81 TYR cc_start: 0.8090 (m-80) cc_final: 0.7756 (m-10) REVERT: C 108 TYR cc_start: 0.7922 (m-80) cc_final: 0.7649 (m-80) REVERT: D 89 GLN cc_start: 0.8331 (pp30) cc_final: 0.8058 (pp30) REVERT: D 122 ASP cc_start: 0.8403 (m-30) cc_final: 0.7924 (t0) REVERT: E 105 THR cc_start: 0.7908 (p) cc_final: 0.7647 (p) REVERT: F 94 THR cc_start: 0.8625 (p) cc_final: 0.8165 (t) REVERT: F 102 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6833 (t) REVERT: F 126 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8815 (pttp) REVERT: G 81 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: G 212 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8790 (mmmt) REVERT: H 24 ARG cc_start: 0.8352 (mmp80) cc_final: 0.7794 (mmp-170) REVERT: H 70 ASP cc_start: 0.7324 (m-30) cc_final: 0.6858 (t0) REVERT: H 125 LEU cc_start: 0.9108 (pp) cc_final: 0.8754 (mp) outliers start: 39 outliers final: 33 residues processed: 239 average time/residue: 0.2793 time to fit residues: 94.5566 Evaluate side-chains 234 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 54 TYR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain 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 175 VAL Chi-restraints excluded: chain E residue 177 GLN Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 150 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain G residue 23 CYS 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 H residue 162 SER Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 194 CYS Chi-restraints excluded: chain H residue 195 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 0.0570 chunk 79 optimal weight: 9.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.6682 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= 0.221 Angle : 0.710 13.499 17772 Z= 0.357 Chirality : 0.044 0.182 2006 Planarity : 0.005 0.068 2273 Dihedral : 4.722 17.937 1821 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.57 % Allowed : 18.23 % Favored : 79.19 % 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: 0.18 (0.21), residues: 1671 helix: -0.74 (0.59), residues: 64 sheet: 0.44 (0.18), residues: 795 loop : -0.00 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 148 HIS 0.005 0.001 HIS H 189 PHE 0.024 0.002 PHE G 128 TYR 0.019 0.001 TYR A 54 ARG 0.010 0.001 ARG B 18 ********************** 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 245 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 1.503 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: A 77 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8291 (pttt) REVERT: C 105 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7144 (p) REVERT: C 108 TYR cc_start: 0.7956 (m-80) cc_final: 0.7690 (m-80) REVERT: C 111 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8300 (pp30) REVERT: D 89 GLN cc_start: 0.8314 (pp30) cc_final: 0.8021 (pp30) REVERT: D 122 ASP cc_start: 0.8347 (m-30) cc_final: 0.7954 (t0) REVERT: E 105 THR cc_start: 0.7908 (p) cc_final: 0.7681 (p) REVERT: F 94 THR cc_start: 0.8622 (p) cc_final: 0.8155 (t) REVERT: F 102 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6832 (t) REVERT: F 126 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8828 (pttp) REVERT: G 74 ASP cc_start: 0.8119 (t70) cc_final: 0.7436 (p0) REVERT: H 24 ARG cc_start: 0.8358 (mmp80) cc_final: 0.7807 (mmp-170) REVERT: H 70 ASP cc_start: 0.7153 (m-30) cc_final: 0.6775 (t0) REVERT: H 125 LEU cc_start: 0.9110 (pp) cc_final: 0.8780 (mp) outliers start: 37 outliers final: 34 residues processed: 236 average time/residue: 0.2794 time to fit residues: 93.2636 Evaluate side-chains 237 residues out of total 1437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 38 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 188 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 146 CYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain 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 217 VAL Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 150 VAL 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 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 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 103 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 19 optimal weight: 0.0030 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.100506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.081174 restraints weight = 38112.817| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.43 r_work: 0.3446 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.6827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13074 Z= 0.254 Angle : 0.712 12.964 17772 Z= 0.361 Chirality : 0.044 0.193 2006 Planarity : 0.005 0.065 2273 Dihedral : 4.812 18.853 1821 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.85 % Allowed : 18.09 % Favored : 79.05 % 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: 0.12 (0.21), residues: 1671 helix: -0.69 (0.59), residues: 64 sheet: 0.39 (0.18), residues: 784 loop : -0.05 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 148 HIS 0.005 0.001 HIS H 189 PHE 0.027 0.002 PHE G 152 TYR 0.018 0.002 TYR A 54 ARG 0.011 0.001 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3577.99 seconds wall clock time: 66 minutes 11.44 seconds (3971.44 seconds total)