Starting phenix.real_space_refine on Fri Jul 19 06:26:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unt_42416/07_2024/8unt_42416.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unt_42416/07_2024/8unt_42416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unt_42416/07_2024/8unt_42416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unt_42416/07_2024/8unt_42416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unt_42416/07_2024/8unt_42416.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unt_42416/07_2024/8unt_42416.cif" } resolution = 3.4 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= 0.023 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 42 5.16 5 C 4306 2.51 5 N 1165 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 373": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6712 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1787 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1775 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 118 Conformer: "B" Number of residues, atoms: 236, 1775 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 11, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 118 bond proxies already assigned to first conformer: 1797 Chain: "B" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2413 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 345 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2119 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 119 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.36, per 1000 atoms: 0.80 Number of scatterers: 6712 At special positions: 0 Unit cell: (82.4315, 135.361, 98.9178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 3 15.00 O 1196 8.00 N 1165 7.00 C 4306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.04 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: 2.35 Conformation dependent library (CDL) restraints added in 1.6 seconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 48.1% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.727A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.564A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.113A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.653A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.635A 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 'G' and resid 9 through 24 removed outlier: 4.144A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.590A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.817A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 66 removed outlier: 5.465A pdb=" N THR R 66 " --> pdb=" O ARG R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.255A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.047A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.677A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.727A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.745A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.786A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 4.329A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.527A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.531A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.565A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.210A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.259A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.683A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.020A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.539A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.150A 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: 3.846A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.787A 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: 3.913A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.333A 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: 3.702A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.952A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1050 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: 1.87 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1551 1.33 - 1.45: 1573 1.45 - 1.58: 3672 1.58 - 1.70: 5 1.70 - 1.82: 57 Bond restraints: 6858 Sorted by residual: bond pdb=" CA ALA R 271 " pdb=" C ALA R 271 " ideal model delta sigma weight residual 1.523 1.470 0.054 1.30e-02 5.92e+03 1.71e+01 bond pdb=" N LYS R 273 " pdb=" CA LYS R 273 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.19e-02 7.06e+03 1.13e+01 bond pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.75e+00 bond pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.68e+00 bond pdb=" CA ILE R 277 " pdb=" C ILE R 277 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.27e-02 6.20e+03 8.35e+00 ... (remaining 6853 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.67: 154 106.67 - 113.59: 3815 113.59 - 120.52: 2725 120.52 - 127.44: 2607 127.44 - 134.36: 77 Bond angle restraints: 9378 Sorted by residual: angle pdb=" N TYR A 253 " pdb=" CA TYR A 253 " pdb=" C TYR A 253 " ideal model delta sigma weight residual 113.97 105.77 8.20 1.28e+00 6.10e-01 4.10e+01 angle pdb=" C ILE R 277 " pdb=" N ILE R 278 " pdb=" CA ILE R 278 " ideal model delta sigma weight residual 122.63 115.03 7.60 1.19e+00 7.06e-01 4.08e+01 angle pdb=" CA GLY A 49 " pdb=" C GLY A 49 " pdb=" O GLY A 49 " ideal model delta sigma weight residual 121.58 116.71 4.87 9.00e-01 1.23e+00 2.93e+01 angle pdb=" N ILE A 62 " pdb=" CA ILE A 62 " pdb=" C ILE A 62 " ideal model delta sigma weight residual 110.62 105.23 5.39 1.02e+00 9.61e-01 2.80e+01 angle pdb=" N PHE A 315 " pdb=" CA PHE A 315 " pdb=" C PHE A 315 " ideal model delta sigma weight residual 111.71 105.79 5.92 1.15e+00 7.56e-01 2.65e+01 ... (remaining 9373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.57: 3898 33.57 - 67.13: 65 67.13 - 100.70: 3 100.70 - 134.26: 0 134.26 - 167.83: 4 Dihedral angle restraints: 3970 sinusoidal: 1302 harmonic: 2668 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -63.24 167.83 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -129.48 -161.25 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 84.26 -153.18 1 2.00e+01 2.50e-03 4.54e+01 ... (remaining 3967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 824 0.047 - 0.093: 195 0.093 - 0.140: 69 0.140 - 0.187: 20 0.187 - 0.234: 9 Chirality restraints: 1117 Sorted by residual: chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASP A 223 " pdb=" N ASP A 223 " pdb=" C ASP A 223 " pdb=" CB ASP A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 224 " pdb=" N VAL A 224 " pdb=" C VAL A 224 " pdb=" CB VAL A 224 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1114 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 44 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C LEU A 44 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU A 44 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 45 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 33 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C VAL R 33 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL R 33 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL R 34 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 315 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C PHE A 315 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE A 315 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 316 " 0.012 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1233 2.77 - 3.30: 6256 3.30 - 3.84: 10500 3.84 - 4.37: 11540 4.37 - 4.90: 21136 Nonbonded interactions: 50665 Sorted by model distance: nonbonded pdb=" N GLU A 50 " pdb=" O3G GTP A 401 " model vdw 2.241 2.520 nonbonded pdb=" N SER A 51 " pdb=" O3G GTP A 401 " model vdw 2.275 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.296 2.440 nonbonded pdb=" O LEU A 63 " pdb=" C HIS A 64 " model vdw 2.330 3.270 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.357 2.520 ... (remaining 50660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.49 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.530 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.005 0.054 6858 Z= 0.350 Angle : 0.808 13.863 9378 Z= 0.520 Chirality : 0.052 0.234 1117 Planarity : 0.004 0.064 1175 Dihedral : 14.498 167.830 2232 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.32 % Allowed : 0.97 % Favored : 98.71 % 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: 1.29 (0.28), residues: 900 helix: 2.15 (0.27), residues: 392 sheet: 1.01 (0.41), residues: 168 loop : -0.79 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.001 PHE A 222 TYR 0.015 0.001 TYR B 59 ARG 0.006 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.741 Fit side-chains REVERT: A 222 PHE cc_start: 0.8370 (m-80) cc_final: 0.8134 (m-80) REVERT: A 295 ASP cc_start: 0.8008 (p0) cc_final: 0.7742 (p0) REVERT: A 314 GLU cc_start: 0.6428 (mm-30) cc_final: 0.6221 (tp30) outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.2014 time to fit residues: 28.2838 Evaluate side-chains 85 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 269 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6858 Z= 0.203 Angle : 0.501 6.200 9378 Z= 0.270 Chirality : 0.041 0.148 1117 Planarity : 0.003 0.035 1175 Dihedral : 10.401 159.888 1006 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.46 % Allowed : 7.93 % Favored : 90.61 % 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: 1.29 (0.29), residues: 900 helix: 2.17 (0.27), residues: 402 sheet: 0.56 (0.41), residues: 173 loop : -0.65 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.021 0.001 PHE A 208 TYR 0.013 0.001 TYR B 59 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.790 Fit side-chains REVERT: A 57 VAL cc_start: 0.8356 (t) cc_final: 0.8137 (p) REVERT: A 314 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6361 (tp30) outliers start: 9 outliers final: 9 residues processed: 96 average time/residue: 0.1999 time to fit residues: 25.3895 Evaluate side-chains 94 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 170 GLN Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 79 optimal weight: 0.9980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6858 Z= 0.150 Angle : 0.461 6.553 9378 Z= 0.246 Chirality : 0.040 0.143 1117 Planarity : 0.003 0.038 1175 Dihedral : 9.792 153.462 1006 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.62 % Allowed : 9.55 % Favored : 88.83 % 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: 1.43 (0.29), residues: 900 helix: 2.29 (0.26), residues: 404 sheet: 0.53 (0.41), residues: 173 loop : -0.54 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.001 HIS A 220 PHE 0.017 0.001 PHE A 208 TYR 0.009 0.001 TYR A 339 ARG 0.007 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.750 Fit side-chains REVERT: A 57 VAL cc_start: 0.8280 (t) cc_final: 0.8068 (p) REVERT: A 222 PHE cc_start: 0.8149 (m-80) cc_final: 0.7905 (m-80) REVERT: A 314 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6401 (tp30) outliers start: 10 outliers final: 10 residues processed: 93 average time/residue: 0.1914 time to fit residues: 23.9369 Evaluate side-chains 94 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 84 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 50.0000 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6858 Z= 0.218 Angle : 0.481 6.718 9378 Z= 0.258 Chirality : 0.041 0.150 1117 Planarity : 0.003 0.038 1175 Dihedral : 9.312 153.478 1004 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.43 % Allowed : 10.03 % Favored : 87.54 % 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: 1.46 (0.29), residues: 900 helix: 2.33 (0.26), residues: 405 sheet: 0.42 (0.40), residues: 179 loop : -0.49 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE A 208 TYR 0.012 0.001 TYR A 339 ARG 0.007 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.739 Fit side-chains REVERT: A 57 VAL cc_start: 0.8279 (t) cc_final: 0.8060 (p) REVERT: R 111 SER cc_start: 0.8722 (t) cc_final: 0.8472 (m) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.2111 time to fit residues: 26.9119 Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6858 Z= 0.263 Angle : 0.514 6.580 9378 Z= 0.276 Chirality : 0.042 0.152 1117 Planarity : 0.003 0.040 1175 Dihedral : 8.882 151.375 1004 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.24 % Allowed : 10.68 % Favored : 86.08 % 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: 1.24 (0.29), residues: 900 helix: 2.18 (0.26), residues: 405 sheet: 0.25 (0.41), residues: 178 loop : -0.60 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE A 208 TYR 0.014 0.001 TYR A 339 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.751 Fit side-chains REVERT: A 57 VAL cc_start: 0.8303 (t) cc_final: 0.8093 (p) REVERT: B 278 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: R 111 SER cc_start: 0.8825 (t) cc_final: 0.8589 (m) outliers start: 20 outliers final: 17 residues processed: 95 average time/residue: 0.1720 time to fit residues: 22.5053 Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6858 Z= 0.157 Angle : 0.460 7.272 9378 Z= 0.244 Chirality : 0.040 0.144 1117 Planarity : 0.003 0.040 1175 Dihedral : 8.428 146.267 1004 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.75 % Allowed : 11.97 % Favored : 85.28 % 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: 1.39 (0.29), residues: 900 helix: 2.35 (0.26), residues: 403 sheet: 0.31 (0.41), residues: 177 loop : -0.57 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.002 0.001 HIS A 357 PHE 0.013 0.001 PHE A 208 TYR 0.010 0.001 TYR A 339 ARG 0.005 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.692 Fit side-chains REVERT: R 111 SER cc_start: 0.8757 (t) cc_final: 0.8509 (m) outliers start: 17 outliers final: 15 residues processed: 88 average time/residue: 0.1716 time to fit residues: 20.8134 Evaluate side-chains 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 318 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 0.0770 chunk 16 optimal weight: 10.0000 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6858 Z= 0.154 Angle : 0.452 6.916 9378 Z= 0.239 Chirality : 0.040 0.143 1117 Planarity : 0.003 0.040 1175 Dihedral : 8.039 146.430 1004 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.75 % Allowed : 13.27 % Favored : 83.98 % 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: 1.44 (0.29), residues: 900 helix: 2.38 (0.26), residues: 405 sheet: 0.27 (0.41), residues: 178 loop : -0.51 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS A 220 PHE 0.012 0.001 PHE A 208 TYR 0.009 0.001 TYR A 339 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.692 Fit side-chains REVERT: A 368 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: B 234 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: R 111 SER cc_start: 0.8709 (t) cc_final: 0.8463 (m) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.1732 time to fit residues: 21.2927 Evaluate side-chains 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6858 Z= 0.197 Angle : 0.470 6.534 9378 Z= 0.251 Chirality : 0.041 0.145 1117 Planarity : 0.003 0.039 1175 Dihedral : 8.027 147.194 1004 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.07 % Allowed : 13.59 % Favored : 83.33 % 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: 1.38 (0.29), residues: 900 helix: 2.33 (0.26), residues: 405 sheet: 0.20 (0.41), residues: 178 loop : -0.51 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.003 0.001 HIS A 220 PHE 0.011 0.001 PHE A 208 TYR 0.011 0.001 TYR A 339 ARG 0.008 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.942 Fit side-chains REVERT: A 368 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: B 234 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 278 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: R 79 ASP cc_start: 0.8940 (t0) cc_final: 0.8595 (t0) REVERT: R 111 SER cc_start: 0.8767 (t) cc_final: 0.8521 (m) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.1826 time to fit residues: 22.8140 Evaluate side-chains 95 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 269 HIS Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 75 optimal weight: 0.3980 chunk 79 optimal weight: 0.0060 chunk 52 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6858 Z= 0.114 Angle : 0.431 7.139 9378 Z= 0.227 Chirality : 0.040 0.137 1117 Planarity : 0.003 0.040 1175 Dihedral : 7.784 145.821 1004 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.27 % Allowed : 14.40 % Favored : 83.33 % 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: 1.56 (0.29), residues: 900 helix: 2.48 (0.26), residues: 405 sheet: 0.36 (0.41), residues: 177 loop : -0.46 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.003 0.000 HIS A 220 PHE 0.012 0.001 PHE A 208 TYR 0.007 0.001 TYR A 339 ARG 0.007 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.704 Fit side-chains REVERT: R 111 SER cc_start: 0.8660 (t) cc_final: 0.8421 (m) outliers start: 14 outliers final: 13 residues processed: 93 average time/residue: 0.1605 time to fit residues: 20.8271 Evaluate side-chains 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.0020 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6858 Z= 0.129 Angle : 0.434 6.934 9378 Z= 0.229 Chirality : 0.040 0.138 1117 Planarity : 0.003 0.039 1175 Dihedral : 7.738 146.723 1004 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.59 % Allowed : 14.40 % Favored : 83.01 % 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: 1.59 (0.29), residues: 900 helix: 2.50 (0.26), residues: 405 sheet: 0.36 (0.41), residues: 178 loop : -0.43 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.002 0.000 HIS A 357 PHE 0.011 0.001 PHE A 208 TYR 0.008 0.001 TYR A 339 ARG 0.007 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.659 Fit side-chains REVERT: R 79 ASP cc_start: 0.8915 (t0) cc_final: 0.8651 (t0) REVERT: R 111 SER cc_start: 0.8664 (t) cc_final: 0.8431 (m) outliers start: 16 outliers final: 16 residues processed: 91 average time/residue: 0.1600 time to fit residues: 20.4404 Evaluate side-chains 98 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106065 restraints weight = 39326.063| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.93 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6858 Z= 0.154 Angle : 0.443 6.748 9378 Z= 0.234 Chirality : 0.040 0.140 1117 Planarity : 0.003 0.039 1175 Dihedral : 7.755 148.340 1004 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.75 % Allowed : 14.08 % Favored : 83.17 % 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: 1.57 (0.29), residues: 900 helix: 2.51 (0.26), residues: 404 sheet: 0.30 (0.41), residues: 179 loop : -0.44 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.002 0.001 HIS A 357 PHE 0.010 0.001 PHE A 208 TYR 0.009 0.001 TYR A 339 ARG 0.007 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.48 seconds wall clock time: 30 minutes 14.19 seconds (1814.19 seconds total)