Starting phenix.real_space_refine on Wed Sep 25 15:43:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/09_2024/7y67_33636_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/09_2024/7y67_33636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/09_2024/7y67_33636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/09_2024/7y67_33636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/09_2024/7y67_33636_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/09_2024/7y67_33636_neut.cif" } resolution = 2.8 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2047 atoms to isotropic. 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 59 5.16 5 C 5675 2.51 5 N 1514 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8889 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1803 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2197 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 53 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'ZAL:plan-1': 1, 'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Time building chain proxies: 5.53, per 1000 atoms: 0.62 Number of scatterers: 8889 At special positions: 0 Unit cell: (95.2, 123.25, 132.6, 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 59 16.00 O 1641 8.00 N 1514 7.00 C 5675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAR L 6 " Input volumes are d-peptide like pdb=" CB ZAL L 4 " Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.7% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.734A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.488A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.857A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.165A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.605A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.736A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.653A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.562A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 65 removed outlier: 3.650A pdb=" N ILE D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 39 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 3.784A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.795A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 110 Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.749A pdb=" N TYR D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.778A pdb=" N CYS D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 174 removed outlier: 3.679A pdb=" N ALA D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 196 through 231 Proline residue: D 214 - end of helix Processing helix chain 'D' and resid 238 through 268 removed outlier: 3.503A pdb=" N LYS D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Proline residue: D 257 - end of helix removed outlier: 3.591A pdb=" N MET D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 288 removed outlier: 4.560A pdb=" N SER D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.946A pdb=" N CYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Proline residue: D 297 - end of helix removed outlier: 3.933A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.565A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.520A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.137A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.655A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.282A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.875A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.573A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.875A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.897A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.958A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.551A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.568A pdb=" N VAL D 190 " --> pdb=" O LYS L 2 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS L 2 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.834A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.072A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 414 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2858 1.35 - 1.47: 2244 1.47 - 1.58: 3891 1.58 - 1.70: 1 1.70 - 1.82: 83 Bond restraints: 9077 Sorted by residual: bond pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N ARG A 208 " pdb=" CA ARG A 208 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.30e-02 5.92e+03 7.66e+00 bond pdb=" CB PRO S 75 " pdb=" CG PRO S 75 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.39e+00 bond pdb=" CE1 HIS D 100 " pdb=" NE2 HIS D 100 " ideal model delta sigma weight residual 1.321 1.338 -0.017 1.00e-02 1.00e+04 2.81e+00 bond pdb=" N LYS D 279 " pdb=" CA LYS D 279 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.30e-02 5.92e+03 2.60e+00 ... (remaining 9072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.86: 12279 4.86 - 9.73: 17 9.73 - 14.59: 0 14.59 - 19.46: 0 19.46 - 24.32: 3 Bond angle restraints: 12299 Sorted by residual: angle pdb=" O MEA L 1 " pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 123.00 99.93 23.07 1.60e+00 3.91e-01 2.08e+02 angle pdb=" CA MEA L 1 " pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 116.20 140.52 -24.32 2.00e+00 2.50e-01 1.48e+02 angle pdb=" C MEA L 1 " pdb=" N LYS L 2 " pdb=" CA LYS L 2 " ideal model delta sigma weight residual 121.70 142.91 -21.21 1.80e+00 3.09e-01 1.39e+02 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.77e+01 angle pdb=" N LYS D 279 " pdb=" CA LYS D 279 " pdb=" C LYS D 279 " ideal model delta sigma weight residual 112.23 106.24 5.99 1.26e+00 6.30e-01 2.26e+01 ... (remaining 12294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.34: 5130 25.34 - 50.67: 218 50.67 - 76.01: 14 76.01 - 101.35: 5 101.35 - 126.68: 1 Dihedral angle restraints: 5368 sinusoidal: 2086 harmonic: 3282 Sorted by residual: dihedral pdb=" CD DAR L 6 " pdb=" NE DAR L 6 " pdb=" CZ DAR L 6 " pdb=" NH1 DAR L 6 " ideal model delta sinusoidal sigma weight residual 0.00 -126.68 126.68 1 1.00e+01 1.00e-02 1.53e+02 dihedral pdb=" CA ZAL L 4 " pdb=" C ZAL L 4 " pdb=" N TRP L 5 " pdb=" CA TRP L 5 " ideal model delta harmonic sigma weight residual 180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TRP B 297 " pdb=" C TRP B 297 " pdb=" N ASP B 298 " pdb=" CA ASP B 298 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 853 0.030 - 0.059: 338 0.059 - 0.089: 128 0.089 - 0.119: 67 0.119 - 0.148: 16 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA HIS D 100 " pdb=" N HIS D 100 " pdb=" C HIS D 100 " pdb=" CB HIS D 100 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" C1 ZAL L 4 " pdb=" CB ZAL L 4 " pdb=" C2 ZAL L 4 " pdb=" C6 ZAL L 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1399 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD DAR L 6 " -0.905 9.50e-02 1.11e+02 4.06e-01 9.95e+01 pdb=" NE DAR L 6 " 0.052 2.00e-02 2.50e+03 pdb=" CZ DAR L 6 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 DAR L 6 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 DAR L 6 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.078 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO S 75 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MEA L 1 " -0.022 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C MEA L 1 " 0.060 2.00e-02 2.50e+03 pdb=" O MEA L 1 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS L 2 " -0.021 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1178 2.76 - 3.47: 11769 3.47 - 4.19: 19275 4.19 - 4.90: 35114 Nonbonded interactions: 67338 Sorted by model distance: nonbonded pdb=" C TRP L 5 " pdb=" N DAR L 6 " model vdw 1.329 3.350 nonbonded pdb=" O THR A 327 " pdb=" OD1 ASP A 328 " model vdw 1.877 3.040 nonbonded pdb=" O ZAL L 4 " pdb=" O TRP L 5 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.227 3.040 nonbonded pdb=" O TRP L 5 " pdb=" N DAR L 6 " model vdw 2.248 3.120 ... (remaining 67333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.003 0.105 9077 Z= 0.199 Angle : 0.691 24.323 12299 Z= 0.388 Chirality : 0.042 0.148 1402 Planarity : 0.011 0.406 1548 Dihedral : 13.096 126.683 3242 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.10 % Allowed : 0.21 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1114 helix: 2.03 (0.28), residues: 367 sheet: 0.71 (0.31), residues: 296 loop : -1.25 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 5 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.001 PHE S 177 TYR 0.018 0.001 TYR D 300 ARG 0.007 0.000 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7670 (tp) cc_final: 0.7431 (tp) REVERT: A 25 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6417 (tm-30) REVERT: A 26 ASP cc_start: 0.6825 (m-30) cc_final: 0.6336 (m-30) REVERT: A 33 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6639 (mm-30) REVERT: A 197 LYS cc_start: 0.7350 (tppt) cc_final: 0.6909 (tptp) REVERT: A 248 LYS cc_start: 0.7453 (ttpp) cc_final: 0.7105 (mtpp) REVERT: A 252 SER cc_start: 0.7869 (m) cc_final: 0.7645 (m) REVERT: A 261 ASP cc_start: 0.6431 (t0) cc_final: 0.6159 (t0) REVERT: B 212 ASP cc_start: 0.7003 (t70) cc_final: 0.6750 (t0) REVERT: B 217 MET cc_start: 0.6469 (ppp) cc_final: 0.6085 (ppp) REVERT: B 237 ASN cc_start: 0.7553 (t0) cc_final: 0.7343 (t0) REVERT: B 331 SER cc_start: 0.8069 (p) cc_final: 0.7802 (p) REVERT: D 282 ASP cc_start: 0.7911 (t70) cc_final: 0.7541 (t70) REVERT: S 21 SER cc_start: 0.8323 (m) cc_final: 0.8028 (p) REVERT: S 119 VAL cc_start: 0.8728 (t) cc_final: 0.8411 (p) REVERT: S 193 SER cc_start: 0.7595 (m) cc_final: 0.7336 (t) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 1.0935 time to fit residues: 250.6453 Evaluate side-chains 173 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 125 ASN B 340 ASN C 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9077 Z= 0.146 Angle : 0.514 6.332 12299 Z= 0.268 Chirality : 0.041 0.136 1402 Planarity : 0.004 0.062 1548 Dihedral : 6.682 177.797 1235 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.66 % Allowed : 12.99 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1114 helix: 2.05 (0.27), residues: 382 sheet: 0.64 (0.31), residues: 290 loop : -1.24 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 211 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE B 234 TYR 0.016 0.001 TYR S 190 ARG 0.008 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 177 time to evaluate : 1.015 Fit side-chains REVERT: A 23 LEU cc_start: 0.7654 (tp) cc_final: 0.7427 (tp) REVERT: A 25 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6432 (tm-30) REVERT: A 26 ASP cc_start: 0.6888 (m-30) cc_final: 0.6475 (m-30) REVERT: A 229 ASP cc_start: 0.7021 (m-30) cc_final: 0.6804 (t0) REVERT: A 248 LYS cc_start: 0.7463 (ttpp) cc_final: 0.7097 (mtpp) REVERT: A 252 SER cc_start: 0.7814 (m) cc_final: 0.7612 (m) REVERT: A 261 ASP cc_start: 0.6419 (t0) cc_final: 0.6146 (t0) REVERT: B 187 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8227 (t) REVERT: B 212 ASP cc_start: 0.7004 (t70) cc_final: 0.6786 (t0) REVERT: B 217 MET cc_start: 0.6576 (ppp) cc_final: 0.6173 (ppp) REVERT: B 237 ASN cc_start: 0.7535 (t0) cc_final: 0.7289 (t0) REVERT: D 253 ILE cc_start: 0.7934 (mt) cc_final: 0.7696 (pt) REVERT: D 263 ILE cc_start: 0.7902 (tp) cc_final: 0.7660 (tp) REVERT: D 282 ASP cc_start: 0.7865 (t70) cc_final: 0.7525 (t70) REVERT: S 6 GLU cc_start: 0.7491 (mp0) cc_final: 0.6849 (mp0) REVERT: S 21 SER cc_start: 0.8346 (m) cc_final: 0.8078 (p) REVERT: S 119 VAL cc_start: 0.8646 (t) cc_final: 0.8385 (p) REVERT: S 154 SER cc_start: 0.8512 (p) cc_final: 0.8293 (m) REVERT: S 192 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7725 (ttp) outliers start: 16 outliers final: 8 residues processed: 187 average time/residue: 1.1079 time to fit residues: 221.6494 Evaluate side-chains 183 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.0570 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.0020 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 overall best weight: 0.4306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 125 ASN C 59 ASN D 145 GLN S 142 GLN S 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9077 Z= 0.147 Angle : 0.493 6.984 12299 Z= 0.259 Chirality : 0.040 0.130 1402 Planarity : 0.003 0.052 1548 Dihedral : 6.488 177.543 1235 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.39 % Allowed : 14.55 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1114 helix: 2.16 (0.27), residues: 382 sheet: 0.65 (0.31), residues: 296 loop : -1.21 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 47 HIS 0.004 0.001 HIS A 188 PHE 0.014 0.001 PHE A 189 TYR 0.020 0.001 TYR D 300 ARG 0.009 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 0.896 Fit side-chains REVERT: A 25 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6485 (tm-30) REVERT: A 26 ASP cc_start: 0.6920 (m-30) cc_final: 0.6591 (m-30) REVERT: A 33 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6619 (mm-30) REVERT: A 248 LYS cc_start: 0.7483 (ttpp) cc_final: 0.7136 (mtpp) REVERT: A 252 SER cc_start: 0.7848 (m) cc_final: 0.7642 (m) REVERT: A 261 ASP cc_start: 0.6408 (t0) cc_final: 0.6130 (t0) REVERT: A 304 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7700 (tt0) REVERT: B 187 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8187 (t) REVERT: B 212 ASP cc_start: 0.7015 (t70) cc_final: 0.6803 (t70) REVERT: B 217 MET cc_start: 0.6610 (ppp) cc_final: 0.6170 (ppp) REVERT: B 254 ASP cc_start: 0.7310 (t70) cc_final: 0.7031 (t0) REVERT: D 131 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7920 (p) REVERT: D 282 ASP cc_start: 0.7914 (t70) cc_final: 0.7571 (t70) REVERT: S 21 SER cc_start: 0.8290 (m) cc_final: 0.8026 (p) REVERT: S 119 VAL cc_start: 0.8709 (t) cc_final: 0.8406 (p) REVERT: S 192 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7720 (ttp) outliers start: 23 outliers final: 8 residues processed: 192 average time/residue: 1.0691 time to fit residues: 219.7669 Evaluate side-chains 187 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS B 75 GLN B 125 ASN B 237 ASN C 44 HIS C 59 ASN D 145 GLN S 35 HIS S 186 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9077 Z= 0.275 Angle : 0.582 7.522 12299 Z= 0.308 Chirality : 0.043 0.138 1402 Planarity : 0.004 0.047 1548 Dihedral : 6.704 179.135 1235 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.70 % Allowed : 17.57 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1114 helix: 2.17 (0.27), residues: 375 sheet: 0.66 (0.31), residues: 295 loop : -1.34 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 47 HIS 0.006 0.002 HIS B 62 PHE 0.018 0.002 PHE A 189 TYR 0.023 0.002 TYR D 300 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6673 (tm-30) REVERT: A 229 ASP cc_start: 0.7161 (m-30) cc_final: 0.6958 (t0) REVERT: A 248 LYS cc_start: 0.7466 (ttpp) cc_final: 0.7171 (mtpp) REVERT: A 261 ASP cc_start: 0.6518 (t0) cc_final: 0.6271 (t0) REVERT: A 277 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7691 (ttmt) REVERT: A 304 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7762 (tt0) REVERT: B 187 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8234 (t) REVERT: B 212 ASP cc_start: 0.7048 (t70) cc_final: 0.6825 (t70) REVERT: B 217 MET cc_start: 0.6615 (ppp) cc_final: 0.6290 (ppp) REVERT: B 254 ASP cc_start: 0.7390 (t70) cc_final: 0.7078 (t0) REVERT: B 303 ASP cc_start: 0.7123 (m-30) cc_final: 0.6886 (m-30) REVERT: D 82 ASP cc_start: 0.6409 (OUTLIER) cc_final: 0.6122 (t70) REVERT: D 131 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7855 (p) REVERT: D 263 ILE cc_start: 0.7896 (tp) cc_final: 0.7692 (tp) REVERT: D 282 ASP cc_start: 0.8056 (t70) cc_final: 0.7762 (t70) REVERT: S 119 VAL cc_start: 0.8681 (t) cc_final: 0.8363 (p) REVERT: S 192 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7865 (ttp) REVERT: S 243 THR cc_start: 0.7879 (t) cc_final: 0.7580 (m) outliers start: 26 outliers final: 13 residues processed: 202 average time/residue: 1.0903 time to fit residues: 235.8257 Evaluate side-chains 192 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 75 GLN B 237 ASN C 59 ASN D 145 GLN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9077 Z= 0.171 Angle : 0.511 10.059 12299 Z= 0.269 Chirality : 0.041 0.129 1402 Planarity : 0.003 0.044 1548 Dihedral : 6.568 179.355 1235 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.81 % Allowed : 19.96 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1114 helix: 2.15 (0.27), residues: 382 sheet: 0.67 (0.31), residues: 290 loop : -1.33 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS B 54 PHE 0.015 0.001 PHE A 189 TYR 0.019 0.001 TYR D 300 ARG 0.004 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 0.931 Fit side-chains REVERT: A 197 LYS cc_start: 0.7698 (tppp) cc_final: 0.7338 (mmmm) REVERT: A 229 ASP cc_start: 0.7106 (m-30) cc_final: 0.6828 (t0) REVERT: A 261 ASP cc_start: 0.6509 (t0) cc_final: 0.6250 (t0) REVERT: A 304 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7720 (tt0) REVERT: B 187 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8200 (t) REVERT: B 212 ASP cc_start: 0.7068 (t70) cc_final: 0.6850 (t70) REVERT: B 217 MET cc_start: 0.6591 (ppp) cc_final: 0.6280 (ppp) REVERT: B 254 ASP cc_start: 0.7373 (t70) cc_final: 0.7065 (t0) REVERT: B 303 ASP cc_start: 0.7085 (m-30) cc_final: 0.6857 (m-30) REVERT: D 82 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.6098 (t70) REVERT: D 263 ILE cc_start: 0.7879 (tp) cc_final: 0.7650 (tp) REVERT: D 282 ASP cc_start: 0.8011 (t70) cc_final: 0.7713 (t70) REVERT: S 21 SER cc_start: 0.8382 (m) cc_final: 0.8149 (p) REVERT: S 119 VAL cc_start: 0.8690 (t) cc_final: 0.8369 (p) REVERT: S 192 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7885 (ttp) outliers start: 27 outliers final: 16 residues processed: 203 average time/residue: 1.0786 time to fit residues: 234.6818 Evaluate side-chains 204 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 40.0000 chunk 103 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9077 Z= 0.205 Angle : 0.543 12.572 12299 Z= 0.282 Chirality : 0.042 0.132 1402 Planarity : 0.003 0.042 1548 Dihedral : 6.588 179.998 1235 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.91 % Allowed : 20.79 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1114 helix: 2.12 (0.27), residues: 382 sheet: 0.64 (0.31), residues: 290 loop : -1.38 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS B 54 PHE 0.015 0.002 PHE A 189 TYR 0.018 0.002 TYR D 300 ARG 0.005 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.043 Fit side-chains REVERT: A 197 LYS cc_start: 0.7731 (tppp) cc_final: 0.7385 (mmmm) REVERT: A 229 ASP cc_start: 0.7098 (m-30) cc_final: 0.6827 (t0) REVERT: A 261 ASP cc_start: 0.6513 (t0) cc_final: 0.6251 (t0) REVERT: A 304 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7729 (tt0) REVERT: B 187 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8228 (t) REVERT: B 217 MET cc_start: 0.6575 (ppp) cc_final: 0.6267 (ppp) REVERT: B 254 ASP cc_start: 0.7402 (t70) cc_final: 0.7085 (t0) REVERT: B 303 ASP cc_start: 0.7110 (m-30) cc_final: 0.6880 (m-30) REVERT: D 82 ASP cc_start: 0.6368 (OUTLIER) cc_final: 0.6069 (t70) REVERT: D 131 SER cc_start: 0.8090 (OUTLIER) cc_final: 0.7887 (p) REVERT: D 263 ILE cc_start: 0.7863 (tp) cc_final: 0.7635 (tp) REVERT: D 282 ASP cc_start: 0.8033 (t70) cc_final: 0.7695 (t70) REVERT: S 21 SER cc_start: 0.8377 (m) cc_final: 0.8155 (p) REVERT: S 25 SER cc_start: 0.8218 (m) cc_final: 0.7745 (p) REVERT: S 119 VAL cc_start: 0.8694 (t) cc_final: 0.8354 (p) REVERT: S 192 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7878 (ttp) outliers start: 28 outliers final: 14 residues processed: 203 average time/residue: 1.0742 time to fit residues: 233.7753 Evaluate side-chains 205 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9077 Z= 0.251 Angle : 0.571 13.239 12299 Z= 0.299 Chirality : 0.043 0.133 1402 Planarity : 0.004 0.041 1548 Dihedral : 6.658 179.153 1235 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.91 % Allowed : 21.10 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1114 helix: 2.09 (0.27), residues: 383 sheet: 0.61 (0.30), residues: 301 loop : -1.46 (0.25), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.005 0.001 HIS B 54 PHE 0.016 0.002 PHE A 189 TYR 0.018 0.002 TYR D 300 ARG 0.008 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 0.865 Fit side-chains REVERT: A 229 ASP cc_start: 0.7106 (m-30) cc_final: 0.6843 (t0) REVERT: A 261 ASP cc_start: 0.6549 (t0) cc_final: 0.6297 (t0) REVERT: A 304 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7749 (tt0) REVERT: B 217 MET cc_start: 0.6564 (ppp) cc_final: 0.6321 (ppp) REVERT: B 254 ASP cc_start: 0.7420 (t70) cc_final: 0.7095 (t0) REVERT: B 303 ASP cc_start: 0.7107 (m-30) cc_final: 0.6884 (m-30) REVERT: D 82 ASP cc_start: 0.6384 (OUTLIER) cc_final: 0.6089 (t70) REVERT: D 206 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7760 (ttp-170) REVERT: D 263 ILE cc_start: 0.7854 (tp) cc_final: 0.7628 (tp) REVERT: D 282 ASP cc_start: 0.8053 (t70) cc_final: 0.7723 (t70) REVERT: S 21 SER cc_start: 0.8373 (m) cc_final: 0.8165 (p) REVERT: S 25 SER cc_start: 0.8223 (m) cc_final: 0.7790 (p) REVERT: S 119 VAL cc_start: 0.8683 (t) cc_final: 0.8345 (p) REVERT: S 192 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7876 (ttp) outliers start: 28 outliers final: 20 residues processed: 203 average time/residue: 1.1238 time to fit residues: 243.6570 Evaluate side-chains 203 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.0570 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 93 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9077 Z= 0.131 Angle : 0.509 13.519 12299 Z= 0.264 Chirality : 0.041 0.140 1402 Planarity : 0.003 0.040 1548 Dihedral : 6.491 178.907 1235 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 22.14 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1114 helix: 2.30 (0.27), residues: 382 sheet: 0.69 (0.31), residues: 298 loop : -1.40 (0.25), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 176 HIS 0.004 0.001 HIS A 188 PHE 0.012 0.001 PHE A 189 TYR 0.015 0.001 TYR D 300 ARG 0.004 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 0.950 Fit side-chains REVERT: A 198 MET cc_start: 0.7952 (ttp) cc_final: 0.7709 (ttp) REVERT: A 261 ASP cc_start: 0.6469 (t0) cc_final: 0.6224 (t0) REVERT: A 304 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7723 (tt0) REVERT: B 217 MET cc_start: 0.6668 (ppp) cc_final: 0.6411 (ppp) REVERT: B 254 ASP cc_start: 0.7383 (t70) cc_final: 0.7073 (t0) REVERT: B 303 ASP cc_start: 0.7024 (m-30) cc_final: 0.6796 (m-30) REVERT: D 82 ASP cc_start: 0.6386 (OUTLIER) cc_final: 0.6073 (t70) REVERT: D 206 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7754 (ttp-170) REVERT: D 236 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.8038 (ttm-80) REVERT: D 263 ILE cc_start: 0.7825 (tp) cc_final: 0.7593 (tp) REVERT: D 282 ASP cc_start: 0.8005 (t70) cc_final: 0.7646 (t70) REVERT: S 21 SER cc_start: 0.8352 (m) cc_final: 0.8145 (p) REVERT: S 25 SER cc_start: 0.8184 (m) cc_final: 0.7687 (p) REVERT: S 119 VAL cc_start: 0.8681 (t) cc_final: 0.8347 (p) REVERT: S 177 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6246 (p90) REVERT: S 192 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7850 (ttp) outliers start: 21 outliers final: 14 residues processed: 196 average time/residue: 1.1222 time to fit residues: 235.0740 Evaluate side-chains 205 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.0470 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9077 Z= 0.177 Angle : 0.528 13.702 12299 Z= 0.275 Chirality : 0.041 0.137 1402 Planarity : 0.003 0.039 1548 Dihedral : 6.480 178.285 1235 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.98 % Allowed : 23.28 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1114 helix: 2.30 (0.27), residues: 382 sheet: 0.74 (0.31), residues: 292 loop : -1.42 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.006 0.001 HIS A 188 PHE 0.014 0.001 PHE A 189 TYR 0.016 0.001 TYR D 300 ARG 0.005 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 0.931 Fit side-chains REVERT: A 229 ASP cc_start: 0.7025 (m-30) cc_final: 0.6814 (t0) REVERT: A 261 ASP cc_start: 0.6493 (t0) cc_final: 0.6249 (t0) REVERT: A 304 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7751 (tt0) REVERT: B 217 MET cc_start: 0.6646 (ppp) cc_final: 0.6366 (ppp) REVERT: B 254 ASP cc_start: 0.7411 (t70) cc_final: 0.7090 (t0) REVERT: B 303 ASP cc_start: 0.7060 (m-30) cc_final: 0.6837 (m-30) REVERT: D 82 ASP cc_start: 0.6352 (OUTLIER) cc_final: 0.6054 (t70) REVERT: D 206 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7744 (ttp-170) REVERT: D 236 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.8046 (ttm-80) REVERT: D 263 ILE cc_start: 0.7818 (tp) cc_final: 0.7589 (tp) REVERT: D 282 ASP cc_start: 0.8047 (t70) cc_final: 0.7677 (t70) REVERT: S 21 SER cc_start: 0.8343 (m) cc_final: 0.8125 (p) REVERT: S 25 SER cc_start: 0.8203 (m) cc_final: 0.7716 (p) REVERT: S 119 VAL cc_start: 0.8685 (t) cc_final: 0.8335 (p) REVERT: S 177 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.6207 (p90) REVERT: S 192 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7865 (ttp) outliers start: 19 outliers final: 12 residues processed: 200 average time/residue: 1.1057 time to fit residues: 236.3524 Evaluate side-chains 198 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 0.0170 chunk 88 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN C 59 ASN D 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9077 Z= 0.153 Angle : 0.521 14.021 12299 Z= 0.268 Chirality : 0.041 0.135 1402 Planarity : 0.003 0.039 1548 Dihedral : 6.449 178.359 1235 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.66 % Allowed : 23.80 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1114 helix: 2.36 (0.27), residues: 382 sheet: 0.72 (0.31), residues: 292 loop : -1.40 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 176 HIS 0.005 0.001 HIS A 188 PHE 0.014 0.001 PHE A 189 TYR 0.015 0.001 TYR D 300 ARG 0.004 0.000 ARG B 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.027 Fit side-chains REVERT: A 229 ASP cc_start: 0.7011 (m-30) cc_final: 0.6752 (t0) REVERT: A 261 ASP cc_start: 0.6480 (t0) cc_final: 0.6235 (t0) REVERT: A 304 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7753 (tt0) REVERT: B 217 MET cc_start: 0.6644 (ppp) cc_final: 0.6333 (ppp) REVERT: B 254 ASP cc_start: 0.7390 (t70) cc_final: 0.7077 (t0) REVERT: B 303 ASP cc_start: 0.7044 (m-30) cc_final: 0.6817 (m-30) REVERT: D 82 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.6046 (t70) REVERT: D 206 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7747 (ttp-170) REVERT: D 236 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.8054 (ttm-80) REVERT: D 263 ILE cc_start: 0.7823 (tp) cc_final: 0.7593 (tp) REVERT: D 282 ASP cc_start: 0.8025 (t70) cc_final: 0.7666 (t70) REVERT: S 21 SER cc_start: 0.8320 (m) cc_final: 0.8107 (p) REVERT: S 25 SER cc_start: 0.8183 (m) cc_final: 0.7691 (p) REVERT: S 119 VAL cc_start: 0.8695 (t) cc_final: 0.8351 (p) REVERT: S 177 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6089 (p90) REVERT: S 192 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7863 (ttp) outliers start: 16 outliers final: 13 residues processed: 190 average time/residue: 1.1536 time to fit residues: 234.2550 Evaluate side-chains 196 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.128719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106978 restraints weight = 12973.714| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.01 r_work: 0.3310 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9077 Z= 0.238 Angle : 0.572 13.764 12299 Z= 0.297 Chirality : 0.042 0.138 1402 Planarity : 0.004 0.038 1548 Dihedral : 6.595 177.928 1235 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.18 % Allowed : 23.49 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1114 helix: 2.26 (0.27), residues: 383 sheet: 0.63 (0.30), residues: 300 loop : -1.43 (0.25), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.006 0.001 HIS A 188 PHE 0.016 0.002 PHE A 189 TYR 0.016 0.002 TYR D 300 ARG 0.008 0.000 ARG S 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4082.12 seconds wall clock time: 71 minutes 32.39 seconds (4292.39 seconds total)