Starting phenix.real_space_refine on Sun Mar 10 22:20:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/03_2024/7td6_25824.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/03_2024/7td6_25824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/03_2024/7td6_25824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/03_2024/7td6_25824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/03_2024/7td6_25824.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td6_25824/03_2024/7td6_25824.pdb" } resolution = 3.0 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= 0.000 sd= 0.003 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 45 5.16 5 C 3460 2.51 5 N 1010 2.21 5 O 1060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5575 Number of models: 1 Model: "" Number of chains: 5 Chain: "1" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1115 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "A" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1115 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "B" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1115 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "C" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1115 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "D" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1115 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Time building chain proxies: 3.39, per 1000 atoms: 0.61 Number of scatterers: 5575 At special positions: 0 Unit cell: (105.73, 112.27, 53.41, 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 45 16.00 O 1060 8.00 N 1010 7.00 C 3460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS 1 178 " - pdb=" SG CYS 1 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 178 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 178 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 178 " - pdb=" SG CYS D 213 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1270 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 94 through 99 removed outlier: 6.507A pdb=" N THR 1 94 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLN B 97 " --> pdb=" O THR 1 94 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN 1 96 " --> pdb=" O GLN B 97 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ASN B 99 " --> pdb=" O ASN 1 96 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP 1 98 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS 1 95 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TRP A 98 " --> pdb=" O HIS 1 95 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN 1 97 " --> pdb=" O TRP A 98 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS A 95 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TRP C 98 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLN A 97 " --> pdb=" O TRP C 98 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N HIS C 95 " --> pdb=" O ASN D 96 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N TRP D 98 " --> pdb=" O HIS C 95 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN C 97 " --> pdb=" O TRP D 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 112 removed outlier: 7.125A pdb=" N HIS B 110 " --> pdb=" O LYS 1 109 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL 1 111 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA B 112 " --> pdb=" O VAL 1 111 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR 1 106 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N LYS A 109 " --> pdb=" O THR 1 106 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N LEU 1 108 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 111 " --> pdb=" O LEU 1 108 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N HIS 1 110 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR A 106 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LYS C 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N LEU A 108 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL C 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N HIS A 110 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR C 106 " --> pdb=" O ASN D 107 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LYS D 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N LEU C 108 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL D 111 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N HIS C 110 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 120 through 121 Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 134 removed outlier: 6.336A pdb=" N MET 1 128 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N SER B 131 " --> pdb=" O MET 1 128 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY 1 130 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N MET B 133 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ALA 1 132 " --> pdb=" O MET B 133 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER 1 131 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 132 " --> pdb=" O SER 1 131 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET 1 133 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N SER A 134 " --> pdb=" O MET 1 133 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N SER A 131 " --> pdb=" O GLY C 130 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA C 132 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET A 133 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SER C 134 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER C 131 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA D 132 " --> pdb=" O SER C 131 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET C 133 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER D 134 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 139 removed outlier: 6.333A pdb=" N MET 1 137 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.516A pdb=" N ASP 1 143 " --> pdb=" O TRP B 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 154 through 155 removed outlier: 6.812A pdb=" N TYR 1 154 " --> pdb=" O ARG B 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 162 removed outlier: 6.448A pdb=" N GLN 1 159 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR A 162 " --> pdb=" O GLN 1 159 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR 1 161 " --> pdb=" O TYR A 162 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN A 159 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR C 162 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR A 161 " --> pdb=" O TYR C 162 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN C 159 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N TYR D 162 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR C 161 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 172 removed outlier: 6.465A pdb=" N GLN 1 167 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ASN B 170 " --> pdb=" O GLN 1 167 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N SER 1 169 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN B 172 " --> pdb=" O SER 1 169 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N GLN 1 171 " --> pdb=" O ASN B 172 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLN A 171 " --> pdb=" O ASN 1 170 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN 1 172 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLN C 171 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASN A 172 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLN D 171 " --> pdb=" O ASN C 170 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN C 172 " --> pdb=" O GLN D 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 189 removed outlier: 6.899A pdb=" N ASN 1 180 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL 1 179 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N THR A 182 " --> pdb=" O VAL 1 179 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE 1 181 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LYS A 184 " --> pdb=" O ILE 1 181 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE 1 183 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N HIS A 186 " --> pdb=" O ILE 1 183 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN 1 185 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL A 188 " --> pdb=" O GLN 1 185 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR 1 187 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 179 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N THR C 182 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 181 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LYS C 184 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 183 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N HIS C 186 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN A 185 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL C 188 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 187 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL C 179 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N THR D 182 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE C 181 " --> pdb=" O THR D 182 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LYS D 184 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 183 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N HIS D 186 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN C 185 " --> pdb=" O HIS D 186 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL D 188 " --> pdb=" O GLN C 185 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR C 187 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 198 through 206 removed outlier: 6.238A pdb=" N GLU 1 199 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL A 202 " --> pdb=" O GLU 1 199 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP 1 201 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N MET A 204 " --> pdb=" O ASP 1 201 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS 1 203 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N GLU A 206 " --> pdb=" O LYS 1 203 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N MET 1 205 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU A 199 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL C 202 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP A 201 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N MET C 204 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 203 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N GLU C 206 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET A 205 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU C 199 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL D 202 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP C 201 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 218 through 219 removed outlier: 6.374A pdb=" N GLN 1 218 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN A 218 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLN C 218 " --> pdb=" O LYS D 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 222 through 225 removed outlier: 6.275A pdb=" N ALA 1 223 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA A 223 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA C 223 " --> pdb=" O TYR D 224 " (cutoff:3.500A) 65 hydrogen bonds defined for protein. 195 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: 1.39 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1875 1.34 - 1.46: 1337 1.46 - 1.58: 2418 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 5710 Sorted by residual: bond pdb=" C ASP B 166 " pdb=" N GLN B 167 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.40e-02 5.10e+03 7.22e-01 bond pdb=" C ASP D 166 " pdb=" N GLN D 167 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.40e-02 5.10e+03 7.19e-01 bond pdb=" C ASP C 166 " pdb=" N GLN C 167 " ideal model delta sigma weight residual 1.330 1.342 -0.012 1.40e-02 5.10e+03 6.90e-01 bond pdb=" C ASP 1 166 " pdb=" N GLN 1 167 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.40e-02 5.10e+03 6.26e-01 bond pdb=" C ASP A 166 " pdb=" N GLN A 167 " ideal model delta sigma weight residual 1.330 1.341 -0.011 1.40e-02 5.10e+03 6.03e-01 ... (remaining 5705 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.40: 262 107.40 - 114.04: 2967 114.04 - 120.68: 2144 120.68 - 127.31: 2277 127.31 - 133.95: 70 Bond angle restraints: 7720 Sorted by residual: angle pdb=" N ASN B 180 " pdb=" CA ASN B 180 " pdb=" C ASN B 180 " ideal model delta sigma weight residual 111.28 116.08 -4.80 1.35e+00 5.49e-01 1.26e+01 angle pdb=" N ASN A 180 " pdb=" CA ASN A 180 " pdb=" C ASN A 180 " ideal model delta sigma weight residual 111.28 116.07 -4.79 1.35e+00 5.49e-01 1.26e+01 angle pdb=" N ASN 1 180 " pdb=" CA ASN 1 180 " pdb=" C ASN 1 180 " ideal model delta sigma weight residual 111.28 116.04 -4.76 1.35e+00 5.49e-01 1.24e+01 angle pdb=" N ASN D 180 " pdb=" CA ASN D 180 " pdb=" C ASN D 180 " ideal model delta sigma weight residual 111.28 116.04 -4.76 1.35e+00 5.49e-01 1.24e+01 angle pdb=" N ASN C 180 " pdb=" CA ASN C 180 " pdb=" C ASN C 180 " ideal model delta sigma weight residual 111.28 116.01 -4.73 1.35e+00 5.49e-01 1.23e+01 ... (remaining 7715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.38: 2946 15.38 - 30.77: 279 30.77 - 46.15: 110 46.15 - 61.53: 40 61.53 - 76.92: 25 Dihedral angle restraints: 3400 sinusoidal: 1390 harmonic: 2010 Sorted by residual: dihedral pdb=" CA ASP A 201 " pdb=" CB ASP A 201 " pdb=" CG ASP A 201 " pdb=" OD1 ASP A 201 " ideal model delta sinusoidal sigma weight residual -30.00 -81.89 51.89 1 2.00e+01 2.50e-03 9.19e+00 dihedral pdb=" CA ASP C 201 " pdb=" CB ASP C 201 " pdb=" CG ASP C 201 " pdb=" OD1 ASP C 201 " ideal model delta sinusoidal sigma weight residual -30.00 -81.87 51.87 1 2.00e+01 2.50e-03 9.18e+00 dihedral pdb=" CA ASP 1 201 " pdb=" CB ASP 1 201 " pdb=" CG ASP 1 201 " pdb=" OD1 ASP 1 201 " ideal model delta sinusoidal sigma weight residual -30.00 -81.87 51.87 1 2.00e+01 2.50e-03 9.18e+00 ... (remaining 3397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 516 0.036 - 0.072: 147 0.072 - 0.108: 86 0.108 - 0.145: 26 0.145 - 0.181: 5 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA ASN B 180 " pdb=" N ASN B 180 " pdb=" C ASN B 180 " pdb=" CB ASN B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA ASN A 180 " pdb=" N ASN A 180 " pdb=" C ASN A 180 " pdb=" CB ASN A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA ASN 1 180 " pdb=" N ASN 1 180 " pdb=" C ASN 1 180 " pdb=" CB ASN 1 180 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 777 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 217 " -0.005 2.00e-02 2.50e+03 4.37e-03 3.82e-01 pdb=" CG TYR D 217 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 217 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 217 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 217 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 217 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 217 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 217 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 217 " -0.006 2.00e-02 2.50e+03 4.33e-03 3.75e-01 pdb=" CG TYR B 217 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 217 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 217 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 217 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 217 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 217 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 217 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 217 " -0.006 2.00e-02 2.50e+03 4.31e-03 3.71e-01 pdb=" CG TYR 1 217 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 217 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 217 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 217 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 217 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR 1 217 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR 1 217 " 0.000 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2165 2.94 - 3.43: 5104 3.43 - 3.92: 9900 3.92 - 4.41: 10113 4.41 - 4.90: 18108 Nonbonded interactions: 45390 Sorted by model distance: nonbonded pdb=" OE1 GLU B 145 " pdb=" NH2 ARG B 150 " model vdw 2.449 2.520 nonbonded pdb=" OE1 GLU C 145 " pdb=" NH2 ARG C 150 " model vdw 2.449 2.520 nonbonded pdb=" OE1 GLU 1 145 " pdb=" NH2 ARG 1 150 " model vdw 2.449 2.520 nonbonded pdb=" OE1 GLU A 145 " pdb=" NH2 ARG A 150 " model vdw 2.449 2.520 nonbonded pdb=" OE1 GLU D 145 " pdb=" NH2 ARG D 150 " model vdw 2.450 2.520 ... (remaining 45385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '1' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.440 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: 0.000 Extract box with map and model: 10.580 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.970 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.002 0.020 5710 Z= 0.126 Angle : 0.570 5.341 7720 Z= 0.350 Chirality : 0.049 0.181 780 Planarity : 0.001 0.012 1020 Dihedral : 16.473 76.917 2115 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.11 (0.27), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 144 HIS 0.001 0.000 HIS A 110 PHE 0.009 0.001 PHE B 174 TYR 0.010 0.001 TYR B 217 ARG 0.001 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 0.689 Fit side-chains REVERT: 1 153 MET cc_start: 0.7616 (mmm) cc_final: 0.7408 (mmm) REVERT: 1 220 GLU cc_start: 0.8457 (mp0) cc_final: 0.7958 (mp0) REVERT: 1 226 ASP cc_start: 0.7652 (m-30) cc_final: 0.7089 (p0) REVERT: A 224 TYR cc_start: 0.7614 (m-80) cc_final: 0.7379 (m-80) REVERT: B 151 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7071 (pm20) REVERT: B 155 ARG cc_start: 0.7969 (mtt180) cc_final: 0.6605 (mmp-170) REVERT: B 163 ARG cc_start: 0.8144 (mtt180) cc_final: 0.6928 (mmp-170) REVERT: B 175 VAL cc_start: 0.8551 (t) cc_final: 0.8148 (m) REVERT: B 199 GLU cc_start: 0.8007 (mp0) cc_final: 0.7556 (mp0) REVERT: B 207 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6030 (ppt90) REVERT: B 212 MET cc_start: 0.8166 (tpp) cc_final: 0.7840 (ttm) REVERT: B 219 LYS cc_start: 0.8094 (mttt) cc_final: 0.6418 (pmtt) REVERT: B 220 GLU cc_start: 0.8054 (mp0) cc_final: 0.7338 (pp20) REVERT: B 221 SER cc_start: 0.8904 (m) cc_final: 0.8403 (m) REVERT: C 128 MET cc_start: 0.8796 (mtp) cc_final: 0.8456 (mtp) REVERT: C 155 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7245 (mtp85) REVERT: C 215 THR cc_start: 0.8787 (m) cc_final: 0.8521 (t) REVERT: C 220 GLU cc_start: 0.8455 (mp0) cc_final: 0.8002 (mp0) REVERT: C 226 ASP cc_start: 0.7721 (m-30) cc_final: 0.7145 (p0) REVERT: D 100 LYS cc_start: 0.7426 (mtmt) cc_final: 0.6745 (mmtt) REVERT: D 135 ARG cc_start: 0.7626 (mtt180) cc_final: 0.7247 (tpm170) REVERT: D 140 PHE cc_start: 0.7749 (m-80) cc_final: 0.6770 (p90) REVERT: D 143 ASP cc_start: 0.8149 (t0) cc_final: 0.7946 (m-30) REVERT: D 153 MET cc_start: 0.8006 (mmm) cc_final: 0.6871 (ptt) REVERT: D 155 ARG cc_start: 0.7800 (mtt180) cc_final: 0.6756 (ptt-90) REVERT: D 163 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7261 (pmt170) REVERT: D 207 ARG cc_start: 0.7603 (mtt180) cc_final: 0.6783 (mmp-170) REVERT: D 212 MET cc_start: 0.8244 (tpp) cc_final: 0.6896 (pmt) REVERT: D 217 TYR cc_start: 0.8499 (p90) cc_final: 0.7999 (p90) REVERT: D 219 LYS cc_start: 0.8071 (mttt) cc_final: 0.7761 (mmtt) REVERT: D 222 GLN cc_start: 0.8555 (mp-120) cc_final: 0.8158 (mp10) REVERT: D 224 TYR cc_start: 0.7638 (m-80) cc_final: 0.7131 (m-80) REVERT: D 229 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7277 (pmt170) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 1.4984 time to fit residues: 309.2389 Evaluate side-chains 155 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 185 GLN 1 211 GLN A 158 ASN A 172 ASN A 185 GLN A 211 GLN B 158 ASN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN B 211 GLN C 172 ASN C 185 GLN C 211 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 5710 Z= 0.611 Angle : 0.791 7.201 7720 Z= 0.436 Chirality : 0.054 0.155 780 Planarity : 0.004 0.029 1020 Dihedral : 5.912 24.317 780 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.03 % Allowed : 14.79 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.62 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 144 HIS 0.008 0.002 HIS 1 110 PHE 0.027 0.004 PHE 1 197 TYR 0.030 0.003 TYR C 217 ARG 0.006 0.001 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.630 Fit side-chains REVERT: 1 100 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7735 (mttp) REVERT: 1 137 MET cc_start: 0.8259 (ttm) cc_final: 0.7876 (ttm) REVERT: 1 153 MET cc_start: 0.7685 (mmm) cc_final: 0.7454 (mmm) REVERT: 1 211 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8653 (mt0) REVERT: 1 219 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7948 (ttmm) REVERT: 1 220 GLU cc_start: 0.8605 (mp0) cc_final: 0.8166 (mp0) REVERT: A 100 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7604 (mttp) REVERT: A 135 ARG cc_start: 0.8166 (ptp-110) cc_final: 0.7872 (ptp90) REVERT: A 155 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7078 (mpp80) REVERT: A 197 PHE cc_start: 0.6892 (m-10) cc_final: 0.6437 (m-10) REVERT: A 211 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: A 224 TYR cc_start: 0.7829 (m-80) cc_final: 0.7471 (m-80) REVERT: A 226 ASP cc_start: 0.7615 (p0) cc_final: 0.7234 (p0) REVERT: B 100 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8097 (mttp) REVERT: B 135 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5500 (pmt-80) REVERT: B 155 ARG cc_start: 0.8096 (mtt180) cc_final: 0.6651 (mmt-90) REVERT: B 206 GLU cc_start: 0.7911 (tp30) cc_final: 0.7542 (tm-30) REVERT: B 207 ARG cc_start: 0.7583 (mtt180) cc_final: 0.6100 (tmm160) REVERT: B 211 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8678 (mt0) REVERT: B 212 MET cc_start: 0.8061 (tpp) cc_final: 0.7782 (ttm) REVERT: B 219 LYS cc_start: 0.8254 (mttt) cc_final: 0.7011 (pptt) REVERT: B 220 GLU cc_start: 0.8215 (mp0) cc_final: 0.7448 (pp20) REVERT: C 128 MET cc_start: 0.8968 (mtp) cc_final: 0.8646 (mtp) REVERT: C 137 MET cc_start: 0.8195 (ttm) cc_final: 0.7776 (ttm) REVERT: C 204 MET cc_start: 0.6909 (tmt) cc_final: 0.6604 (tmt) REVERT: C 220 GLU cc_start: 0.8685 (mp0) cc_final: 0.8403 (mp0) REVERT: C 224 TYR cc_start: 0.7997 (m-80) cc_final: 0.7787 (m-80) REVERT: D 100 LYS cc_start: 0.7783 (mtmt) cc_final: 0.6868 (mmmt) REVERT: D 135 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7518 (tpm170) REVERT: D 140 PHE cc_start: 0.8069 (m-80) cc_final: 0.6295 (p90) REVERT: D 155 ARG cc_start: 0.8079 (mtt180) cc_final: 0.6735 (ptt90) REVERT: D 163 ARG cc_start: 0.8632 (mtt180) cc_final: 0.7146 (pmt170) REVERT: D 206 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7508 (tm-30) REVERT: D 207 ARG cc_start: 0.8201 (mtt180) cc_final: 0.6276 (mmp-170) REVERT: D 212 MET cc_start: 0.8456 (tpp) cc_final: 0.7052 (pmt) REVERT: D 221 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8523 (m) REVERT: D 224 TYR cc_start: 0.7999 (m-80) cc_final: 0.7629 (m-80) REVERT: D 226 ASP cc_start: 0.7609 (p0) cc_final: 0.7123 (p0) REVERT: D 229 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7269 (pmt170) outliers start: 18 outliers final: 5 residues processed: 164 average time/residue: 1.5364 time to fit residues: 260.0913 Evaluate side-chains 148 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 131 SER Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 211 GLN Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5710 Z= 0.190 Angle : 0.618 6.286 7720 Z= 0.335 Chirality : 0.049 0.135 780 Planarity : 0.002 0.020 1020 Dihedral : 5.444 20.162 780 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.65 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 98 HIS 0.002 0.001 HIS 1 110 PHE 0.020 0.003 PHE 1 197 TYR 0.026 0.002 TYR 1 217 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.761 Fit side-chains REVERT: 1 133 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6870 (mpt) REVERT: 1 153 MET cc_start: 0.7623 (mmm) cc_final: 0.7388 (mmm) REVERT: A 135 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8114 (ptp90) REVERT: A 195 GLU cc_start: 0.5732 (tm-30) cc_final: 0.5218 (tm-30) REVERT: A 197 PHE cc_start: 0.6342 (m-10) cc_final: 0.5629 (m-10) REVERT: A 224 TYR cc_start: 0.7789 (m-80) cc_final: 0.7382 (m-80) REVERT: B 100 LYS cc_start: 0.8252 (mtmt) cc_final: 0.8037 (mttp) REVERT: B 135 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5776 (pmt-80) REVERT: B 155 ARG cc_start: 0.8027 (mtt180) cc_final: 0.6688 (mmp-170) REVERT: B 207 ARG cc_start: 0.7536 (mtt180) cc_final: 0.6044 (tmm160) REVERT: B 212 MET cc_start: 0.8045 (tpp) cc_final: 0.7755 (ttm) REVERT: B 219 LYS cc_start: 0.8208 (mttt) cc_final: 0.6717 (pmtt) REVERT: B 220 GLU cc_start: 0.8174 (mp0) cc_final: 0.7537 (pp20) REVERT: C 128 MET cc_start: 0.8885 (mtp) cc_final: 0.8562 (mtp) REVERT: C 137 MET cc_start: 0.8095 (ttm) cc_final: 0.7662 (ttm) REVERT: C 195 GLU cc_start: 0.6295 (tm-30) cc_final: 0.5318 (tt0) REVERT: C 197 PHE cc_start: 0.6232 (m-10) cc_final: 0.5934 (m-10) REVERT: C 204 MET cc_start: 0.6825 (tmt) cc_final: 0.6571 (tmt) REVERT: C 220 GLU cc_start: 0.8932 (mp0) cc_final: 0.8303 (mp0) REVERT: D 100 LYS cc_start: 0.7700 (mtmt) cc_final: 0.6913 (mmtt) REVERT: D 133 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6526 (mpt) REVERT: D 135 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7532 (tpm170) REVERT: D 140 PHE cc_start: 0.8051 (m-80) cc_final: 0.6374 (p90) REVERT: D 145 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: D 146 ASP cc_start: 0.7818 (t0) cc_final: 0.7570 (t0) REVERT: D 153 MET cc_start: 0.8351 (mmm) cc_final: 0.6440 (pp-130) REVERT: D 155 ARG cc_start: 0.7924 (mtt180) cc_final: 0.6912 (ptt90) REVERT: D 163 ARG cc_start: 0.8613 (mtt180) cc_final: 0.7064 (pmt170) REVERT: D 206 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7366 (tm-30) REVERT: D 207 ARG cc_start: 0.8145 (mtt180) cc_final: 0.6401 (mmp-170) REVERT: D 212 MET cc_start: 0.8325 (tpp) cc_final: 0.7032 (pmt) REVERT: D 221 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8417 (m) REVERT: D 222 GLN cc_start: 0.8415 (mp-120) cc_final: 0.8113 (mp10) REVERT: D 224 TYR cc_start: 0.7984 (m-80) cc_final: 0.7663 (m-80) REVERT: D 229 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7176 (pmt170) outliers start: 17 outliers final: 5 residues processed: 152 average time/residue: 1.5840 time to fit residues: 248.5625 Evaluate side-chains 142 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 133 MET Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain A residue 135 ARG Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 0.3980 chunk 62 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 211 GLN A 211 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5710 Z= 0.336 Angle : 0.647 8.016 7720 Z= 0.351 Chirality : 0.049 0.144 780 Planarity : 0.003 0.017 1020 Dihedral : 5.633 21.357 780 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.20 % Allowed : 17.14 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.77 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.004 0.001 HIS 1 110 PHE 0.027 0.003 PHE 1 197 TYR 0.030 0.002 TYR C 217 ARG 0.004 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 0.633 Fit side-chains REVERT: 1 133 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6891 (mpt) REVERT: 1 137 MET cc_start: 0.8193 (ttm) cc_final: 0.7875 (ttm) REVERT: 1 153 MET cc_start: 0.7781 (mmm) cc_final: 0.7571 (mmm) REVERT: 1 211 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8812 (mm-40) REVERT: A 197 PHE cc_start: 0.6684 (m-10) cc_final: 0.6258 (m-10) REVERT: A 224 TYR cc_start: 0.7869 (m-80) cc_final: 0.7506 (m-80) REVERT: A 226 ASP cc_start: 0.7585 (p0) cc_final: 0.7212 (p0) REVERT: B 100 LYS cc_start: 0.8346 (mtmt) cc_final: 0.8012 (mttp) REVERT: B 135 ARG cc_start: 0.6139 (OUTLIER) cc_final: 0.5812 (pmt-80) REVERT: B 155 ARG cc_start: 0.8061 (mtt180) cc_final: 0.6616 (mmp-170) REVERT: B 206 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 207 ARG cc_start: 0.7908 (mtt180) cc_final: 0.6190 (tmm160) REVERT: B 210 GLU cc_start: 0.4409 (OUTLIER) cc_final: 0.4110 (pm20) REVERT: B 212 MET cc_start: 0.8054 (tpp) cc_final: 0.7816 (ttm) REVERT: B 219 LYS cc_start: 0.8221 (mttt) cc_final: 0.6753 (pmtt) REVERT: B 220 GLU cc_start: 0.8112 (mp0) cc_final: 0.7544 (pp20) REVERT: C 128 MET cc_start: 0.8939 (mtp) cc_final: 0.8641 (mtp) REVERT: C 137 MET cc_start: 0.8157 (ttm) cc_final: 0.7738 (ttm) REVERT: C 204 MET cc_start: 0.6921 (tmt) cc_final: 0.6718 (tmt) REVERT: C 220 GLU cc_start: 0.8827 (mp0) cc_final: 0.8294 (mp0) REVERT: C 229 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7120 (mtp85) REVERT: D 100 LYS cc_start: 0.7752 (mtmt) cc_final: 0.6919 (mmtt) REVERT: D 133 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6520 (mpt) REVERT: D 135 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7538 (tpm170) REVERT: D 140 PHE cc_start: 0.8056 (m-80) cc_final: 0.6188 (p90) REVERT: D 145 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: D 153 MET cc_start: 0.8356 (mmm) cc_final: 0.6496 (pp-130) REVERT: D 155 ARG cc_start: 0.7929 (mtt180) cc_final: 0.6906 (ptt90) REVERT: D 163 ARG cc_start: 0.8689 (mtt180) cc_final: 0.7102 (pmt170) REVERT: D 207 ARG cc_start: 0.8159 (mtt180) cc_final: 0.6338 (mmp-170) REVERT: D 212 MET cc_start: 0.8352 (tpp) cc_final: 0.7062 (pmt) REVERT: D 221 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8571 (m) REVERT: D 224 TYR cc_start: 0.8023 (m-80) cc_final: 0.7649 (m-80) REVERT: D 229 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7123 (pmt170) outliers start: 25 outliers final: 6 residues processed: 157 average time/residue: 1.6203 time to fit residues: 262.5406 Evaluate side-chains 150 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 133 MET Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 211 GLN A 211 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN C 211 GLN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5710 Z= 0.432 Angle : 0.708 7.880 7720 Z= 0.384 Chirality : 0.050 0.151 780 Planarity : 0.003 0.019 1020 Dihedral : 5.866 22.377 780 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.53 % Allowed : 18.15 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.87 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 98 HIS 0.006 0.001 HIS 1 110 PHE 0.023 0.003 PHE 1 197 TYR 0.031 0.002 TYR C 217 ARG 0.004 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.660 Fit side-chains REVERT: 1 137 MET cc_start: 0.8225 (ttm) cc_final: 0.7889 (ttm) REVERT: 1 211 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8477 (mm-40) REVERT: A 197 PHE cc_start: 0.6790 (m-10) cc_final: 0.6406 (m-10) REVERT: A 211 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: A 224 TYR cc_start: 0.7912 (m-80) cc_final: 0.7613 (m-80) REVERT: A 226 ASP cc_start: 0.7673 (p0) cc_final: 0.7447 (p0) REVERT: A 229 ARG cc_start: 0.8090 (mmt-90) cc_final: 0.7809 (mmt-90) REVERT: B 135 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5805 (pmt-80) REVERT: B 146 ASP cc_start: 0.8392 (t0) cc_final: 0.8178 (t0) REVERT: B 155 ARG cc_start: 0.8088 (mtt180) cc_final: 0.6613 (mmp-170) REVERT: B 206 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7437 (tm-30) REVERT: B 207 ARG cc_start: 0.7838 (mtt180) cc_final: 0.6092 (tmm160) REVERT: B 210 GLU cc_start: 0.4506 (OUTLIER) cc_final: 0.4149 (pm20) REVERT: B 212 MET cc_start: 0.8080 (tpp) cc_final: 0.7775 (ttm) REVERT: B 219 LYS cc_start: 0.8243 (mttt) cc_final: 0.6737 (pmtt) REVERT: B 220 GLU cc_start: 0.8184 (mp0) cc_final: 0.7591 (pp20) REVERT: C 128 MET cc_start: 0.8980 (mtp) cc_final: 0.8678 (mtp) REVERT: C 137 MET cc_start: 0.8145 (ttm) cc_final: 0.7743 (ttm) REVERT: C 195 GLU cc_start: 0.6366 (tm-30) cc_final: 0.5380 (tt0) REVERT: C 204 MET cc_start: 0.6961 (tmt) cc_final: 0.6729 (tmt) REVERT: C 220 GLU cc_start: 0.8785 (mp0) cc_final: 0.8309 (mp0) REVERT: C 229 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7156 (mtp85) REVERT: D 100 LYS cc_start: 0.7802 (mtmt) cc_final: 0.6940 (mmtt) REVERT: D 133 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6473 (mpt) REVERT: D 135 ARG cc_start: 0.7781 (mtt180) cc_final: 0.7446 (tpm170) REVERT: D 140 PHE cc_start: 0.8136 (m-80) cc_final: 0.6167 (p90) REVERT: D 145 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: D 148 TYR cc_start: 0.8122 (p90) cc_final: 0.7911 (p90) REVERT: D 153 MET cc_start: 0.8366 (mmm) cc_final: 0.6492 (pp-130) REVERT: D 155 ARG cc_start: 0.8002 (mtt180) cc_final: 0.6975 (ptt90) REVERT: D 163 ARG cc_start: 0.8738 (mtt180) cc_final: 0.7033 (pmt170) REVERT: D 206 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7386 (tm-30) REVERT: D 207 ARG cc_start: 0.8221 (mtt180) cc_final: 0.6290 (mmp-170) REVERT: D 212 MET cc_start: 0.8362 (tpp) cc_final: 0.7044 (pmt) REVERT: D 221 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8563 (m) REVERT: D 222 GLN cc_start: 0.8527 (mp-120) cc_final: 0.8239 (mp10) REVERT: D 224 TYR cc_start: 0.8040 (m-80) cc_final: 0.7704 (m-80) REVERT: D 229 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7167 (pmt170) outliers start: 21 outliers final: 6 residues processed: 153 average time/residue: 1.6178 time to fit residues: 255.1751 Evaluate side-chains 151 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 211 GLN A 211 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN C 211 GLN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5710 Z= 0.262 Angle : 0.674 7.490 7720 Z= 0.361 Chirality : 0.049 0.142 780 Planarity : 0.003 0.018 1020 Dihedral : 5.697 22.097 780 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.70 % Allowed : 18.49 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.87 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 98 HIS 0.003 0.001 HIS 1 110 PHE 0.020 0.003 PHE 1 197 TYR 0.031 0.002 TYR C 217 ARG 0.003 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 0.669 Fit side-chains REVERT: 1 137 MET cc_start: 0.8239 (ttm) cc_final: 0.7909 (ttm) REVERT: 1 211 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8413 (mm-40) REVERT: A 143 ASP cc_start: 0.8040 (m-30) cc_final: 0.7716 (m-30) REVERT: A 153 MET cc_start: 0.8100 (mmm) cc_final: 0.7870 (mmm) REVERT: A 211 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: A 224 TYR cc_start: 0.7891 (m-80) cc_final: 0.7644 (m-80) REVERT: A 226 ASP cc_start: 0.7565 (p0) cc_final: 0.7313 (p0) REVERT: A 229 ARG cc_start: 0.8104 (mmt-90) cc_final: 0.7820 (mmt-90) REVERT: B 135 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5791 (pmt-80) REVERT: B 146 ASP cc_start: 0.8359 (t0) cc_final: 0.8091 (t0) REVERT: B 155 ARG cc_start: 0.8059 (mtt180) cc_final: 0.6608 (mmp-170) REVERT: B 206 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7425 (tm-30) REVERT: B 207 ARG cc_start: 0.7835 (mtt180) cc_final: 0.6143 (tmm160) REVERT: B 210 GLU cc_start: 0.4481 (OUTLIER) cc_final: 0.4145 (pm20) REVERT: B 212 MET cc_start: 0.8035 (tpp) cc_final: 0.7764 (ttm) REVERT: B 219 LYS cc_start: 0.8187 (mttt) cc_final: 0.6700 (pmtt) REVERT: B 220 GLU cc_start: 0.8227 (mp0) cc_final: 0.7575 (pp20) REVERT: C 128 MET cc_start: 0.8941 (mtp) cc_final: 0.8673 (mtp) REVERT: C 137 MET cc_start: 0.8125 (ttm) cc_final: 0.7762 (ttm) REVERT: C 155 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7647 (mtt180) REVERT: C 204 MET cc_start: 0.6947 (tmt) cc_final: 0.6697 (tmt) REVERT: C 220 GLU cc_start: 0.8786 (mp0) cc_final: 0.8282 (mp0) REVERT: C 229 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7137 (mtp85) REVERT: D 100 LYS cc_start: 0.7786 (mtmt) cc_final: 0.6909 (mmtt) REVERT: D 135 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7350 (tpm170) REVERT: D 140 PHE cc_start: 0.8058 (m-80) cc_final: 0.6113 (p90) REVERT: D 145 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: D 148 TYR cc_start: 0.8016 (p90) cc_final: 0.7808 (p90) REVERT: D 153 MET cc_start: 0.8373 (mmm) cc_final: 0.6521 (pp-130) REVERT: D 155 ARG cc_start: 0.7927 (mtt180) cc_final: 0.6896 (ptt90) REVERT: D 163 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7037 (pmt170) REVERT: D 206 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 207 ARG cc_start: 0.8238 (mtt180) cc_final: 0.6410 (mmp-170) REVERT: D 212 MET cc_start: 0.8283 (tpp) cc_final: 0.6955 (pmt) REVERT: D 221 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 222 GLN cc_start: 0.8574 (mp-120) cc_final: 0.8230 (mp10) REVERT: D 224 TYR cc_start: 0.8044 (m-80) cc_final: 0.7667 (m-80) REVERT: D 229 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7195 (pmt170) outliers start: 22 outliers final: 7 residues processed: 157 average time/residue: 1.5788 time to fit residues: 255.8071 Evaluate side-chains 154 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 196 ASN 1 211 GLN A 211 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN C 211 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5710 Z= 0.257 Angle : 0.686 8.031 7720 Z= 0.366 Chirality : 0.049 0.150 780 Planarity : 0.002 0.018 1020 Dihedral : 5.647 20.970 780 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.70 % Allowed : 18.82 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.89 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 98 HIS 0.003 0.001 HIS 1 110 PHE 0.022 0.003 PHE B 197 TYR 0.032 0.002 TYR C 217 ARG 0.003 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 0.686 Fit side-chains REVERT: 1 137 MET cc_start: 0.8268 (ttm) cc_final: 0.7979 (ttm) REVERT: 1 211 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8337 (mm-40) REVERT: 1 229 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7704 (mtm-85) REVERT: A 143 ASP cc_start: 0.8054 (m-30) cc_final: 0.7740 (m-30) REVERT: A 153 MET cc_start: 0.8136 (mmm) cc_final: 0.7913 (mmm) REVERT: A 211 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: A 224 TYR cc_start: 0.7879 (m-80) cc_final: 0.7636 (m-80) REVERT: A 226 ASP cc_start: 0.7577 (p0) cc_final: 0.7310 (p0) REVERT: A 229 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7824 (mmt-90) REVERT: B 135 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5786 (pmt-80) REVERT: B 146 ASP cc_start: 0.8337 (t0) cc_final: 0.8087 (t0) REVERT: B 155 ARG cc_start: 0.8017 (mtt180) cc_final: 0.6596 (mmp-170) REVERT: B 206 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 207 ARG cc_start: 0.7811 (mtt180) cc_final: 0.6121 (tmm160) REVERT: B 210 GLU cc_start: 0.4379 (OUTLIER) cc_final: 0.4048 (pm20) REVERT: B 212 MET cc_start: 0.8066 (tpp) cc_final: 0.7807 (ttm) REVERT: B 219 LYS cc_start: 0.8178 (mttt) cc_final: 0.6720 (pmtt) REVERT: B 220 GLU cc_start: 0.8214 (mp0) cc_final: 0.7562 (pp20) REVERT: C 128 MET cc_start: 0.8953 (mtp) cc_final: 0.8707 (mtp) REVERT: C 137 MET cc_start: 0.8128 (ttm) cc_final: 0.7760 (ttm) REVERT: C 195 GLU cc_start: 0.6083 (tm-30) cc_final: 0.5601 (tt0) REVERT: C 204 MET cc_start: 0.6959 (tmt) cc_final: 0.6693 (tmt) REVERT: C 220 GLU cc_start: 0.8812 (mp0) cc_final: 0.8274 (mp0) REVERT: C 229 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7118 (mtp85) REVERT: D 100 LYS cc_start: 0.7817 (mtmt) cc_final: 0.6876 (mmtt) REVERT: D 133 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6665 (mpt) REVERT: D 135 ARG cc_start: 0.7746 (mtt180) cc_final: 0.7366 (tpm170) REVERT: D 140 PHE cc_start: 0.8123 (m-80) cc_final: 0.6121 (p90) REVERT: D 145 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: D 153 MET cc_start: 0.8362 (mmm) cc_final: 0.6495 (pp-130) REVERT: D 155 ARG cc_start: 0.7955 (mtt180) cc_final: 0.6922 (ptt90) REVERT: D 163 ARG cc_start: 0.8771 (mtt180) cc_final: 0.7135 (pmt170) REVERT: D 207 ARG cc_start: 0.8235 (mtt180) cc_final: 0.6383 (mmp-170) REVERT: D 212 MET cc_start: 0.8257 (tpp) cc_final: 0.6951 (pmt) REVERT: D 221 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8569 (m) REVERT: D 222 GLN cc_start: 0.8603 (mp-120) cc_final: 0.8213 (mp10) REVERT: D 224 TYR cc_start: 0.8050 (m-80) cc_final: 0.7678 (m-80) REVERT: D 229 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7194 (pmt170) outliers start: 22 outliers final: 9 residues processed: 153 average time/residue: 1.5207 time to fit residues: 240.3352 Evaluate side-chains 156 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 128 MET Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain 1 residue 229 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 196 ASN 1 211 GLN A 211 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5710 Z= 0.338 Angle : 0.731 8.240 7720 Z= 0.391 Chirality : 0.050 0.154 780 Planarity : 0.003 0.022 1020 Dihedral : 5.758 21.811 780 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.87 % Allowed : 19.50 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.94 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 98 HIS 0.004 0.001 HIS 1 110 PHE 0.023 0.003 PHE C 197 TYR 0.033 0.002 TYR C 217 ARG 0.005 0.000 ARG 1 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 0.657 Fit side-chains REVERT: 1 137 MET cc_start: 0.8250 (ttm) cc_final: 0.7918 (ttm) REVERT: 1 211 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8324 (mm-40) REVERT: 1 229 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7726 (mtm-85) REVERT: A 143 ASP cc_start: 0.8062 (m-30) cc_final: 0.7756 (m-30) REVERT: A 153 MET cc_start: 0.8141 (mmm) cc_final: 0.7923 (mmm) REVERT: A 211 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: A 224 TYR cc_start: 0.7871 (m-80) cc_final: 0.7642 (m-80) REVERT: A 226 ASP cc_start: 0.7602 (p0) cc_final: 0.7338 (p0) REVERT: A 229 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7837 (mmt-90) REVERT: B 135 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5758 (pmt-80) REVERT: B 146 ASP cc_start: 0.8341 (t0) cc_final: 0.8029 (t0) REVERT: B 155 ARG cc_start: 0.8017 (mtt180) cc_final: 0.6558 (mmp-170) REVERT: B 206 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7452 (tm-30) REVERT: B 207 ARG cc_start: 0.7831 (mtt180) cc_final: 0.6163 (tmm160) REVERT: B 210 GLU cc_start: 0.4161 (OUTLIER) cc_final: 0.3840 (pm20) REVERT: B 212 MET cc_start: 0.8085 (tpp) cc_final: 0.7841 (ttm) REVERT: B 219 LYS cc_start: 0.8203 (mttt) cc_final: 0.6732 (pmtt) REVERT: B 220 GLU cc_start: 0.8193 (mp0) cc_final: 0.7575 (pp20) REVERT: C 128 MET cc_start: 0.8962 (mtp) cc_final: 0.8711 (mtp) REVERT: C 137 MET cc_start: 0.8144 (ttm) cc_final: 0.7772 (ttm) REVERT: C 155 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7237 (mtt90) REVERT: C 195 GLU cc_start: 0.6396 (tm-30) cc_final: 0.5565 (tt0) REVERT: C 220 GLU cc_start: 0.8845 (mp0) cc_final: 0.8303 (mp0) REVERT: C 229 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7105 (mtp85) REVERT: D 100 LYS cc_start: 0.7838 (mtmt) cc_final: 0.6871 (mmtt) REVERT: D 133 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6651 (mpt) REVERT: D 135 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7375 (tpm170) REVERT: D 140 PHE cc_start: 0.8084 (m-80) cc_final: 0.6013 (p90) REVERT: D 145 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: D 148 TYR cc_start: 0.8014 (p90) cc_final: 0.7759 (p90) REVERT: D 153 MET cc_start: 0.8374 (mmm) cc_final: 0.6468 (pp-130) REVERT: D 155 ARG cc_start: 0.8042 (mtt180) cc_final: 0.6954 (ptt90) REVERT: D 163 ARG cc_start: 0.8758 (mtt180) cc_final: 0.7125 (pmt170) REVERT: D 207 ARG cc_start: 0.8388 (mtt180) cc_final: 0.6261 (mmp-170) REVERT: D 212 MET cc_start: 0.8280 (tpp) cc_final: 0.6946 (pmt) REVERT: D 221 SER cc_start: 0.8871 (OUTLIER) cc_final: 0.8551 (m) REVERT: D 229 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7218 (pmt170) outliers start: 23 outliers final: 8 residues processed: 151 average time/residue: 1.5827 time to fit residues: 246.5535 Evaluate side-chains 155 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain 1 residue 229 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 52 optimal weight: 0.0470 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 211 GLN A 211 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5710 Z= 0.296 Angle : 0.752 8.666 7720 Z= 0.399 Chirality : 0.050 0.164 780 Planarity : 0.002 0.019 1020 Dihedral : 5.778 21.728 780 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.20 % Allowed : 20.17 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.94 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 98 HIS 0.004 0.001 HIS 1 110 PHE 0.030 0.003 PHE 1 197 TYR 0.032 0.002 TYR C 217 ARG 0.003 0.000 ARG 1 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 0.672 Fit side-chains REVERT: 1 137 MET cc_start: 0.8226 (ttm) cc_final: 0.7774 (ttm) REVERT: 1 211 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8285 (mm-40) REVERT: 1 229 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7721 (mtm-85) REVERT: A 153 MET cc_start: 0.8100 (mmm) cc_final: 0.7861 (mmm) REVERT: A 211 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: A 224 TYR cc_start: 0.7854 (m-80) cc_final: 0.7651 (m-80) REVERT: A 226 ASP cc_start: 0.7595 (p0) cc_final: 0.7326 (p0) REVERT: A 229 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7827 (mmt-90) REVERT: B 135 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5683 (pmt-80) REVERT: B 146 ASP cc_start: 0.8353 (t0) cc_final: 0.8059 (t0) REVERT: B 155 ARG cc_start: 0.8024 (mtt180) cc_final: 0.6567 (mmp-170) REVERT: B 206 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 207 ARG cc_start: 0.7761 (mtt180) cc_final: 0.6157 (tmm160) REVERT: B 210 GLU cc_start: 0.4180 (OUTLIER) cc_final: 0.3887 (pm20) REVERT: B 212 MET cc_start: 0.8022 (tpp) cc_final: 0.7770 (ttm) REVERT: B 219 LYS cc_start: 0.8163 (mttt) cc_final: 0.6693 (pmtt) REVERT: B 220 GLU cc_start: 0.8214 (mp0) cc_final: 0.7605 (pp20) REVERT: C 128 MET cc_start: 0.8952 (mtp) cc_final: 0.8662 (mtp) REVERT: C 137 MET cc_start: 0.8131 (ttm) cc_final: 0.7749 (ttm) REVERT: C 155 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7227 (mtt90) REVERT: C 195 GLU cc_start: 0.6301 (tm-30) cc_final: 0.5455 (tt0) REVERT: C 220 GLU cc_start: 0.8847 (mp0) cc_final: 0.8302 (mp0) REVERT: C 229 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7096 (mtp85) REVERT: D 100 LYS cc_start: 0.7912 (mtmt) cc_final: 0.6975 (mmtt) REVERT: D 133 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6624 (mpt) REVERT: D 135 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7382 (tpm170) REVERT: D 140 PHE cc_start: 0.8154 (m-80) cc_final: 0.6007 (p90) REVERT: D 145 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: D 153 MET cc_start: 0.8358 (mmm) cc_final: 0.6469 (pp-130) REVERT: D 155 ARG cc_start: 0.8040 (mtt180) cc_final: 0.6962 (ptt90) REVERT: D 163 ARG cc_start: 0.8708 (mtt180) cc_final: 0.7117 (pmt170) REVERT: D 206 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7552 (tm-30) REVERT: D 207 ARG cc_start: 0.8322 (mtt180) cc_final: 0.6332 (mmp-170) REVERT: D 212 MET cc_start: 0.8249 (tpp) cc_final: 0.6958 (pmt) REVERT: D 221 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8560 (m) REVERT: D 229 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7234 (pmt170) outliers start: 25 outliers final: 12 residues processed: 153 average time/residue: 1.5776 time to fit residues: 249.2967 Evaluate side-chains 157 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 128 MET Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain 1 residue 229 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 211 GLN A 211 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5710 Z= 0.267 Angle : 0.756 8.674 7720 Z= 0.400 Chirality : 0.050 0.168 780 Planarity : 0.003 0.026 1020 Dihedral : 5.748 22.332 780 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.87 % Allowed : 20.50 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.96 (0.25), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 98 HIS 0.003 0.001 HIS 1 110 PHE 0.016 0.002 PHE A 197 TYR 0.032 0.002 TYR C 217 ARG 0.004 0.000 ARG 1 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 0.653 Fit side-chains REVERT: 1 137 MET cc_start: 0.8211 (ttm) cc_final: 0.7862 (ttm) REVERT: 1 211 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8022 (mm-40) REVERT: 1 229 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7712 (mtm-85) REVERT: A 153 MET cc_start: 0.8115 (mmm) cc_final: 0.7870 (mmm) REVERT: A 195 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6268 (tm-30) REVERT: A 211 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: A 226 ASP cc_start: 0.7581 (p0) cc_final: 0.7368 (p0) REVERT: A 229 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7786 (mmt-90) REVERT: B 135 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.5656 (pmt-80) REVERT: B 146 ASP cc_start: 0.8355 (t0) cc_final: 0.8063 (t0) REVERT: B 155 ARG cc_start: 0.8015 (mtt180) cc_final: 0.6561 (mmp-170) REVERT: B 206 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7400 (tm-30) REVERT: B 207 ARG cc_start: 0.7788 (mtt180) cc_final: 0.6205 (tmm160) REVERT: B 210 GLU cc_start: 0.4177 (OUTLIER) cc_final: 0.3893 (pm20) REVERT: B 212 MET cc_start: 0.8028 (tpp) cc_final: 0.7795 (ttm) REVERT: B 219 LYS cc_start: 0.8135 (mttt) cc_final: 0.6676 (pmtt) REVERT: B 220 GLU cc_start: 0.8250 (mp0) cc_final: 0.7623 (pp20) REVERT: C 128 MET cc_start: 0.8956 (mtp) cc_final: 0.8674 (mtp) REVERT: C 137 MET cc_start: 0.8120 (ttm) cc_final: 0.7734 (ttm) REVERT: C 155 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7665 (mtt180) REVERT: C 195 GLU cc_start: 0.6220 (tm-30) cc_final: 0.5430 (tt0) REVERT: C 206 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7721 (tp30) REVERT: C 220 GLU cc_start: 0.8822 (mp0) cc_final: 0.8290 (mp0) REVERT: C 229 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7083 (mtp85) REVERT: D 100 LYS cc_start: 0.7917 (mtmt) cc_final: 0.6997 (mmtt) REVERT: D 133 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6699 (mpt) REVERT: D 135 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7380 (tpm170) REVERT: D 140 PHE cc_start: 0.8151 (m-80) cc_final: 0.6009 (p90) REVERT: D 145 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: D 153 MET cc_start: 0.8313 (mmm) cc_final: 0.6412 (pp-130) REVERT: D 155 ARG cc_start: 0.7978 (mtt180) cc_final: 0.6920 (ptt90) REVERT: D 163 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7123 (pmt170) REVERT: D 206 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7411 (tm-30) REVERT: D 207 ARG cc_start: 0.8343 (mtt180) cc_final: 0.6358 (mmp-170) REVERT: D 212 MET cc_start: 0.8253 (tpp) cc_final: 0.6957 (pmt) REVERT: D 221 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8579 (m) REVERT: D 229 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7187 (pmt170) outliers start: 23 outliers final: 11 residues processed: 149 average time/residue: 1.5634 time to fit residues: 240.5948 Evaluate side-chains 157 residues out of total 595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 128 MET Chi-restraints excluded: chain 1 residue 140 PHE Chi-restraints excluded: chain 1 residue 211 GLN Chi-restraints excluded: chain 1 residue 221 SER Chi-restraints excluded: chain 1 residue 229 ARG Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 221 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 211 GLN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 GLN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 211 GLN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.110654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.094357 restraints weight = 10129.773| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.94 r_work: 0.3842 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5710 Z= 0.356 Angle : 0.782 9.787 7720 Z= 0.414 Chirality : 0.051 0.175 780 Planarity : 0.003 0.023 1020 Dihedral : 5.912 23.559 780 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.03 % Allowed : 20.84 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.02 (0.24), residues: 680 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.19), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 98 HIS 0.005 0.001 HIS 1 110 PHE 0.030 0.003 PHE 1 197 TYR 0.032 0.002 TYR C 217 ARG 0.003 0.000 ARG B 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3877.59 seconds wall clock time: 68 minutes 35.81 seconds (4115.81 seconds total)