Starting phenix.real_space_refine on Fri Nov 15 05:08:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vhf_43236/11_2024/8vhf_43236.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vhf_43236/11_2024/8vhf_43236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vhf_43236/11_2024/8vhf_43236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vhf_43236/11_2024/8vhf_43236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vhf_43236/11_2024/8vhf_43236.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vhf_43236/11_2024/8vhf_43236.cif" } resolution = 3.51 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= -0.003 sd= 0.221 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5258 2.51 5 N 1455 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8299 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "A" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1960 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2289 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 284} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'8VP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.65 Number of scatterers: 8299 At special positions: 0 Unit cell: (73.6, 98.44, 130.64, 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 56 16.00 O 1530 8.00 N 1455 7.00 C 5258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.03 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 40.9% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'B' and resid 13 through 37 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.585A pdb=" N ILE B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.802A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.726A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 39 removed outlier: 4.330A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.834A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.434A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.974A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.810A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'R' and resid 6 through 37 removed outlier: 3.809A pdb=" N ILE R 10 " --> pdb=" O SER R 6 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 66 removed outlier: 4.210A pdb=" N THR R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASP R 64 " --> pdb=" O GLY R 60 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 109 removed outlier: 3.570A pdb=" N CYS R 78 " --> pdb=" O GLN R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 114 Processing helix chain 'R' and resid 118 through 143 Proline residue: R 140 - end of helix Processing helix chain 'R' and resid 163 through 173 removed outlier: 3.566A pdb=" N LEU R 167 " --> pdb=" O PRO R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 209 removed outlier: 3.629A pdb=" N ALA R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 249 removed outlier: 4.020A pdb=" N TRP R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 256 through 263 Processing helix chain 'R' and resid 264 through 280 removed outlier: 3.847A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 300 removed outlier: 3.733A pdb=" N LYS R 299 " --> pdb=" O LEU R 295 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL R 300 " --> pdb=" O GLY R 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.601A pdb=" N ILE B 349 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR B 61 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU B 347 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 73 removed outlier: 3.793A pdb=" N ALA B 71 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B 73 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER B 85 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.561A pdb=" N GLY B 126 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 164 removed outlier: 3.546A pdb=" N CYS B 159 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 163 " --> pdb=" O GLN B 167 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLN B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASP B 181 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLN B 187 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.674A pdb=" N SER B 200 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLN B 231 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP B 223 " --> pdb=" O CYS B 229 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS B 229 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 245 removed outlier: 3.782A pdb=" N MET B 273 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 265 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU B 271 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 289 removed outlier: 6.385A pdb=" N GLY B 299 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 287 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 297 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 289 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 295 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 317 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP B 309 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG B 315 " --> pdb=" O ASP B 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.697A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.684A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 207 through 213 removed outlier: 4.223A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1194 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: 2.27 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: 1.22 - 1.34: 2718 1.34 - 1.46: 1853 1.46 - 1.58: 3817 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8469 Sorted by residual: bond pdb=" C14 8VP R 601 " pdb=" C19 8VP R 601 " ideal model delta sigma weight residual 1.557 1.450 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C3 8VP R 601 " pdb=" N28 8VP R 601 " ideal model delta sigma weight residual 1.423 1.324 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C20 8VP R 601 " pdb=" N17 8VP R 601 " ideal model delta sigma weight residual 1.357 1.448 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C14 8VP R 601 " pdb=" C15 8VP R 601 " ideal model delta sigma weight residual 1.533 1.454 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" N31 8VP R 601 " pdb=" N32 8VP R 601 " ideal model delta sigma weight residual 1.288 1.364 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 8464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 11343 3.30 - 6.59: 100 6.59 - 9.89: 17 9.89 - 13.19: 3 13.19 - 16.49: 2 Bond angle restraints: 11465 Sorted by residual: angle pdb=" CA LEU R 139 " pdb=" CB LEU R 139 " pdb=" CG LEU R 139 " ideal model delta sigma weight residual 116.30 132.79 -16.49 3.50e+00 8.16e-02 2.22e+01 angle pdb=" CA LEU C 19 " pdb=" CB LEU C 19 " pdb=" CG LEU C 19 " ideal model delta sigma weight residual 116.30 131.86 -15.56 3.50e+00 8.16e-02 1.98e+01 angle pdb=" CA ARG A 13 " pdb=" CB ARG A 13 " pdb=" CG ARG A 13 " ideal model delta sigma weight residual 114.10 122.40 -8.30 2.00e+00 2.50e-01 1.72e+01 angle pdb=" CA LYS A 307 " pdb=" CB LYS A 307 " pdb=" CG LYS A 307 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA GLU C 17 " pdb=" CB GLU C 17 " pdb=" CG GLU C 17 " ideal model delta sigma weight residual 114.10 122.15 -8.05 2.00e+00 2.50e-01 1.62e+01 ... (remaining 11460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.99: 4545 23.99 - 47.98: 455 47.98 - 71.97: 47 71.97 - 95.97: 15 95.97 - 119.96: 1 Dihedral angle restraints: 5063 sinusoidal: 2000 harmonic: 3063 Sorted by residual: dihedral pdb=" CB CYS R 78 " pdb=" SG CYS R 78 " pdb=" SG CYS R 155 " pdb=" CB CYS R 155 " ideal model delta sinusoidal sigma weight residual 93.00 176.08 -83.08 1 1.00e+01 1.00e-02 8.44e+01 dihedral pdb=" C16 8VP R 601 " pdb=" C18 8VP R 601 " pdb=" N17 8VP R 601 " pdb=" C19 8VP R 601 " ideal model delta sinusoidal sigma weight residual -60.31 59.65 -119.96 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" CA ASP R 220 " pdb=" C ASP R 220 " pdb=" N PHE R 221 " pdb=" CA PHE R 221 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 968 0.045 - 0.091: 235 0.091 - 0.136: 83 0.136 - 0.181: 3 0.181 - 0.226: 1 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CB ILE R 116 " pdb=" CA ILE R 116 " pdb=" CG1 ILE R 116 " pdb=" CG2 ILE R 116 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU R 77 " pdb=" CB LEU R 77 " pdb=" CD1 LEU R 77 " pdb=" CD2 LEU R 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA ASP R 51 " pdb=" N ASP R 51 " pdb=" C ASP R 51 " pdb=" CB ASP R 51 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 1287 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 215 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" CG ASP A 215 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP A 215 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 215 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 20 " -0.165 9.50e-02 1.11e+02 7.42e-02 3.72e+00 pdb=" NE ARG A 20 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 20 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 20 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 20 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 215 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C ASP A 215 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP A 215 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 216 " 0.011 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1538 2.77 - 3.30: 7924 3.30 - 3.83: 14325 3.83 - 4.37: 15974 4.37 - 4.90: 27864 Nonbonded interactions: 67625 Sorted by model distance: nonbonded pdb=" O SER B 78 " pdb=" OG SER B 78 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 253 " pdb=" O SER A 306 " model vdw 2.280 3.040 nonbonded pdb=" O LYS R 75 " pdb=" OG SER R 79 " model vdw 2.294 3.040 nonbonded pdb=" O TRP N 47 " pdb=" OG1 THR N 61 " model vdw 2.303 3.040 nonbonded pdb=" O SER R 233 " pdb=" OG SER R 237 " model vdw 2.306 3.040 ... (remaining 67620 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 group one per residue 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.860 Find NCS groups from input model: 0.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.004 0.107 8469 Z= 0.285 Angle : 0.823 16.485 11465 Z= 0.409 Chirality : 0.044 0.226 1290 Planarity : 0.004 0.074 1463 Dihedral : 17.720 119.958 3079 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.34 % Allowed : 29.71 % Favored : 69.96 % 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: -0.22 (0.25), residues: 1043 helix: 1.15 (0.26), residues: 396 sheet: -0.31 (0.34), residues: 195 loop : -1.22 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 180 HIS 0.010 0.001 HIS R 292 PHE 0.031 0.001 PHE A 340 TYR 0.012 0.001 TYR B 275 ARG 0.010 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 187 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8552 (tp40) REVERT: N 13 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8274 (mm-40) REVERT: A 27 GLU cc_start: 0.8718 (tp30) cc_final: 0.8486 (tp30) outliers start: 3 outliers final: 0 residues processed: 188 average time/residue: 0.2063 time to fit residues: 53.0343 Evaluate side-chains 177 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8469 Z= 0.200 Angle : 0.586 11.382 11465 Z= 0.295 Chirality : 0.041 0.139 1290 Planarity : 0.004 0.039 1463 Dihedral : 5.623 54.199 1178 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.14 % Allowed : 28.14 % Favored : 68.72 % 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: 0.19 (0.26), residues: 1043 helix: 1.56 (0.26), residues: 404 sheet: -0.29 (0.33), residues: 217 loop : -1.02 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 222 HIS 0.006 0.001 HIS B 236 PHE 0.012 0.001 PHE A 340 TYR 0.011 0.001 TYR A 339 ARG 0.007 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8891 (mmtt) REVERT: B 70 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: B 300 TYR cc_start: 0.8363 (m-80) cc_final: 0.8142 (m-80) REVERT: C 18 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8408 (tp40) REVERT: C 27 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7278 (mmm-85) REVERT: N 13 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8339 (mm-40) REVERT: N 90 ASP cc_start: 0.8864 (t0) cc_final: 0.8606 (t0) REVERT: A 16 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: A 27 GLU cc_start: 0.8744 (tp30) cc_final: 0.8500 (tp30) REVERT: A 253 TYR cc_start: 0.5032 (p90) cc_final: 0.4717 (p90) REVERT: A 390 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7879 (tm-30) REVERT: R 145 MET cc_start: 0.8088 (tpp) cc_final: 0.7608 (tpp) REVERT: R 274 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8333 (tt) outliers start: 28 outliers final: 17 residues processed: 209 average time/residue: 0.1917 time to fit residues: 55.9353 Evaluate side-chains 194 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8469 Z= 0.186 Angle : 0.556 9.148 11465 Z= 0.285 Chirality : 0.041 0.140 1290 Planarity : 0.003 0.036 1463 Dihedral : 5.389 47.183 1178 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.36 % Allowed : 29.48 % Favored : 67.15 % 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: 0.31 (0.26), residues: 1043 helix: 1.73 (0.26), residues: 403 sheet: -0.30 (0.33), residues: 218 loop : -0.99 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 180 HIS 0.007 0.001 HIS R 292 PHE 0.013 0.001 PHE A 340 TYR 0.016 0.001 TYR A 391 ARG 0.002 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: C 18 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8405 (tp40) REVERT: C 27 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7412 (mmm-85) REVERT: N 13 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8382 (mm-40) REVERT: N 90 ASP cc_start: 0.8991 (t0) cc_final: 0.8709 (t0) REVERT: A 16 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: A 27 GLU cc_start: 0.8737 (tp30) cc_final: 0.8477 (tp30) REVERT: A 253 TYR cc_start: 0.5058 (p90) cc_final: 0.4466 (p90) REVERT: A 390 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7921 (tm-30) REVERT: R 145 MET cc_start: 0.8088 (tpp) cc_final: 0.7636 (tpp) REVERT: R 162 HIS cc_start: 0.8246 (t70) cc_final: 0.7876 (t70) REVERT: R 274 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8350 (tt) outliers start: 30 outliers final: 19 residues processed: 206 average time/residue: 0.1873 time to fit residues: 53.7452 Evaluate side-chains 200 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 292 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8469 Z= 0.222 Angle : 0.579 11.436 11465 Z= 0.294 Chirality : 0.041 0.149 1290 Planarity : 0.003 0.037 1463 Dihedral : 5.398 46.707 1178 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.48 % Allowed : 27.47 % Favored : 68.05 % 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: 0.26 (0.26), residues: 1043 helix: 1.67 (0.26), residues: 406 sheet: -0.35 (0.33), residues: 218 loop : -1.01 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 180 HIS 0.007 0.001 HIS R 292 PHE 0.014 0.001 PHE R 157 TYR 0.020 0.001 TYR A 391 ARG 0.002 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: C 18 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8438 (tp40) REVERT: C 27 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7365 (mmm-85) REVERT: N 13 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8372 (mm-40) REVERT: N 73 ASP cc_start: 0.7529 (t0) cc_final: 0.6908 (t70) REVERT: N 90 ASP cc_start: 0.8999 (t0) cc_final: 0.8733 (t0) REVERT: A 16 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: A 27 GLU cc_start: 0.8759 (tp30) cc_final: 0.8502 (tp30) REVERT: A 215 ASP cc_start: 0.7705 (t70) cc_final: 0.7493 (t70) REVERT: A 253 TYR cc_start: 0.5237 (p90) cc_final: 0.5017 (p90) REVERT: A 390 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7882 (tm-30) REVERT: R 145 MET cc_start: 0.8080 (tpp) cc_final: 0.7709 (tpp) REVERT: R 162 HIS cc_start: 0.8309 (t70) cc_final: 0.7955 (t70) REVERT: R 260 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8735 (mp) outliers start: 40 outliers final: 23 residues processed: 208 average time/residue: 0.1938 time to fit residues: 56.2536 Evaluate side-chains 200 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 155 CYS Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 292 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8469 Z= 0.234 Angle : 0.605 8.991 11465 Z= 0.303 Chirality : 0.042 0.143 1290 Planarity : 0.003 0.037 1463 Dihedral : 5.420 46.455 1178 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.26 % Allowed : 28.81 % Favored : 66.93 % 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: 0.28 (0.26), residues: 1043 helix: 1.68 (0.26), residues: 406 sheet: -0.34 (0.32), residues: 223 loop : -0.99 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 180 HIS 0.009 0.001 HIS R 292 PHE 0.016 0.001 PHE A 340 TYR 0.020 0.001 TYR A 391 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: C 18 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8416 (tp40) REVERT: C 21 MET cc_start: 0.8353 (tmm) cc_final: 0.8135 (tmm) REVERT: C 27 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.7474 (mmm-85) REVERT: N 13 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8397 (mm-40) REVERT: N 73 ASP cc_start: 0.7614 (t0) cc_final: 0.7082 (t0) REVERT: N 90 ASP cc_start: 0.9034 (t0) cc_final: 0.8817 (t0) REVERT: A 16 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: A 27 GLU cc_start: 0.8761 (tp30) cc_final: 0.8502 (tp30) REVERT: A 215 ASP cc_start: 0.7826 (t70) cc_final: 0.7544 (t70) REVERT: A 253 TYR cc_start: 0.5305 (p90) cc_final: 0.5078 (p90) REVERT: R 145 MET cc_start: 0.8104 (tpp) cc_final: 0.7698 (tpp) REVERT: R 284 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8580 (mmmt) outliers start: 38 outliers final: 30 residues processed: 203 average time/residue: 0.1959 time to fit residues: 55.4357 Evaluate side-chains 205 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 292 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8469 Z= 0.194 Angle : 0.595 11.771 11465 Z= 0.296 Chirality : 0.041 0.143 1290 Planarity : 0.003 0.036 1463 Dihedral : 5.315 44.504 1178 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.48 % Allowed : 28.92 % Favored : 66.59 % 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: 0.37 (0.26), residues: 1043 helix: 1.81 (0.26), residues: 400 sheet: -0.34 (0.32), residues: 223 loop : -0.93 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 180 HIS 0.008 0.001 HIS B 236 PHE 0.017 0.001 PHE A 340 TYR 0.019 0.001 TYR A 391 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: C 18 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8382 (tp40) REVERT: C 22 GLU cc_start: 0.8569 (pp20) cc_final: 0.8340 (pp20) REVERT: C 27 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.7375 (mmm-85) REVERT: N 13 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8396 (mm-40) REVERT: N 38 ARG cc_start: 0.8710 (ptt180) cc_final: 0.8395 (ptt180) REVERT: N 73 ASP cc_start: 0.7658 (t0) cc_final: 0.7106 (t0) REVERT: A 16 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: A 27 GLU cc_start: 0.8750 (tp30) cc_final: 0.8484 (tp30) REVERT: A 215 ASP cc_start: 0.7852 (t70) cc_final: 0.7549 (t70) REVERT: A 253 TYR cc_start: 0.5502 (p90) cc_final: 0.5219 (p90) REVERT: A 390 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7944 (tm-30) REVERT: R 35 LYS cc_start: 0.8508 (ttpp) cc_final: 0.8283 (mtpt) REVERT: R 260 LEU cc_start: 0.9003 (mp) cc_final: 0.8745 (mt) REVERT: R 284 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8563 (mmmt) outliers start: 40 outliers final: 28 residues processed: 214 average time/residue: 0.1984 time to fit residues: 59.0919 Evaluate side-chains 210 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 272 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 98 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8469 Z= 0.182 Angle : 0.606 13.390 11465 Z= 0.301 Chirality : 0.041 0.136 1290 Planarity : 0.003 0.036 1463 Dihedral : 5.310 41.316 1178 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.48 % Allowed : 29.82 % Favored : 65.70 % 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: 0.38 (0.26), residues: 1043 helix: 1.84 (0.26), residues: 400 sheet: -0.48 (0.32), residues: 225 loop : -0.85 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 180 HIS 0.009 0.001 HIS R 292 PHE 0.019 0.001 PHE R 157 TYR 0.015 0.001 TYR A 391 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: C 18 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8456 (tp40) REVERT: C 27 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7222 (mmm-85) REVERT: N 38 ARG cc_start: 0.8642 (ptt180) cc_final: 0.8421 (ptt180) REVERT: N 73 ASP cc_start: 0.7708 (t0) cc_final: 0.7161 (t0) REVERT: A 16 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: A 215 ASP cc_start: 0.7898 (t70) cc_final: 0.7577 (t70) REVERT: A 390 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7920 (tm-30) REVERT: R 35 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8276 (mtpt) REVERT: R 260 LEU cc_start: 0.9041 (mp) cc_final: 0.8827 (mt) outliers start: 40 outliers final: 28 residues processed: 218 average time/residue: 0.2007 time to fit residues: 61.1378 Evaluate side-chains 215 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 292 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 0.4980 chunk 9 optimal weight: 0.0870 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8469 Z= 0.188 Angle : 0.624 13.489 11465 Z= 0.312 Chirality : 0.041 0.134 1290 Planarity : 0.003 0.036 1463 Dihedral : 5.259 40.535 1178 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.15 % Allowed : 30.04 % Favored : 65.81 % 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: 0.35 (0.26), residues: 1043 helix: 1.78 (0.26), residues: 400 sheet: -0.46 (0.32), residues: 225 loop : -0.85 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 180 HIS 0.013 0.001 HIS R 292 PHE 0.021 0.001 PHE A 340 TYR 0.014 0.001 TYR A 391 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: C 18 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8494 (tp40) REVERT: C 27 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7220 (mmm-85) REVERT: N 38 ARG cc_start: 0.8595 (ptt180) cc_final: 0.8385 (ptt180) REVERT: N 73 ASP cc_start: 0.7708 (t0) cc_final: 0.7169 (t0) REVERT: A 16 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: A 31 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7321 (mt0) REVERT: A 215 ASP cc_start: 0.7890 (t70) cc_final: 0.7555 (t70) REVERT: A 390 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7909 (tm-30) REVERT: R 260 LEU cc_start: 0.9060 (mp) cc_final: 0.8858 (mt) outliers start: 37 outliers final: 29 residues processed: 217 average time/residue: 0.2017 time to fit residues: 61.5129 Evaluate side-chains 218 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 155 CYS Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 292 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8469 Z= 0.200 Angle : 0.636 14.076 11465 Z= 0.317 Chirality : 0.042 0.160 1290 Planarity : 0.003 0.036 1463 Dihedral : 5.279 40.098 1178 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.59 % Allowed : 31.39 % Favored : 65.02 % 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: 0.37 (0.26), residues: 1043 helix: 1.77 (0.26), residues: 400 sheet: -0.41 (0.33), residues: 220 loop : -0.84 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 180 HIS 0.014 0.001 HIS R 292 PHE 0.026 0.001 PHE A 340 TYR 0.015 0.001 TYR R 185 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8826 (mtpp) REVERT: B 70 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: C 18 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8467 (tp40) REVERT: C 27 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7320 (mmm-85) REVERT: N 13 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8295 (mm-40) REVERT: N 38 ARG cc_start: 0.8587 (ptt180) cc_final: 0.8366 (ptt180) REVERT: N 73 ASP cc_start: 0.7733 (t0) cc_final: 0.7190 (t0) REVERT: A 16 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: A 31 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7316 (mt0) REVERT: A 215 ASP cc_start: 0.7909 (t70) cc_final: 0.7568 (t70) REVERT: A 390 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7913 (tm-30) REVERT: R 35 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8322 (mtpt) outliers start: 32 outliers final: 28 residues processed: 206 average time/residue: 0.1880 time to fit residues: 54.2394 Evaluate side-chains 214 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 155 CYS Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 292 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8469 Z= 0.216 Angle : 0.640 14.534 11465 Z= 0.319 Chirality : 0.042 0.158 1290 Planarity : 0.003 0.037 1463 Dihedral : 5.321 40.477 1178 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.48 % Allowed : 31.84 % Favored : 64.69 % 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: 0.34 (0.26), residues: 1043 helix: 1.74 (0.26), residues: 400 sheet: -0.44 (0.32), residues: 226 loop : -0.85 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 180 HIS 0.017 0.001 HIS R 292 PHE 0.027 0.001 PHE A 340 TYR 0.016 0.001 TYR R 185 ARG 0.004 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2086 Ramachandran restraints generated. 1043 Oldfield, 0 Emsley, 1043 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.9124 (mmtt) cc_final: 0.8827 (mtpp) REVERT: B 70 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: B 271 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8025 (tm-30) REVERT: C 18 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8491 (tp40) REVERT: C 27 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7352 (mmm-85) REVERT: N 13 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8299 (mm-40) REVERT: N 38 ARG cc_start: 0.8593 (ptt180) cc_final: 0.8373 (ptt180) REVERT: N 73 ASP cc_start: 0.7759 (t0) cc_final: 0.7218 (t0) REVERT: A 16 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: A 31 GLN cc_start: 0.7828 (tm-30) cc_final: 0.7324 (mt0) REVERT: A 60 MET cc_start: 0.6492 (pmm) cc_final: 0.6242 (pmm) REVERT: A 215 ASP cc_start: 0.7929 (t70) cc_final: 0.7592 (t70) REVERT: A 253 TYR cc_start: 0.4948 (p90) cc_final: 0.4370 (p90) REVERT: A 390 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7910 (tm-30) REVERT: R 35 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8332 (mtpt) REVERT: R 291 TYR cc_start: 0.7897 (t80) cc_final: 0.7643 (t80) outliers start: 31 outliers final: 28 residues processed: 206 average time/residue: 0.2018 time to fit residues: 57.3208 Evaluate side-chains 218 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 56 VAL Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 102 ASP Chi-restraints excluded: chain R residue 155 CYS Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 292 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103261 restraints weight = 13394.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107278 restraints weight = 7284.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109969 restraints weight = 4931.348| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8469 Z= 0.225 Angle : 0.645 14.475 11465 Z= 0.323 Chirality : 0.042 0.154 1290 Planarity : 0.003 0.037 1463 Dihedral : 5.345 40.706 1178 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.04 % Allowed : 31.61 % Favored : 64.35 % 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: 0.33 (0.26), residues: 1043 helix: 1.74 (0.26), residues: 401 sheet: -0.45 (0.32), residues: 226 loop : -0.86 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 180 HIS 0.013 0.001 HIS R 292 PHE 0.024 0.001 PHE A 340 TYR 0.022 0.001 TYR A 391 ARG 0.004 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2037.32 seconds wall clock time: 38 minutes 12.01 seconds (2292.01 seconds total)