Starting phenix.real_space_refine on Mon Nov 18 23:30:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibv_35346/11_2024/8ibv_35346.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibv_35346/11_2024/8ibv_35346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibv_35346/11_2024/8ibv_35346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibv_35346/11_2024/8ibv_35346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibv_35346/11_2024/8ibv_35346.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibv_35346/11_2024/8ibv_35346.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 S 58 5.16 5 C 5759 2.51 5 N 1569 2.21 5 O 1672 1.98 5 H 9023 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18081 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 4539 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 13, 'TRANS': 265} Chain breaks: 3 Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 332 Classifications: {'peptide': 19} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "A" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3815 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 5089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5089 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3479 Classifications: {'peptide': 230} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 827 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Time building chain proxies: 8.67, per 1000 atoms: 0.48 Number of scatterers: 18081 At special positions: 0 Unit cell: (123.6, 91.464, 137.608, 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 58 16.00 O 1672 8.00 N 1569 7.00 C 5759 6.00 H 9023 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 235 " distance=2.02 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: 5.11 Conformation dependent library (CDL) restraints added in 1.8 seconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 38.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'R' and resid 34 through 66 removed outlier: 3.898A pdb=" N VAL R 39 " --> pdb=" O LEU R 35 " (cutoff:3.500A) Proline residue: R 40 - end of helix removed outlier: 3.632A pdb=" N TYR R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 89 Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 107 through 141 removed outlier: 3.645A pdb=" N GLY R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 170 Processing helix chain 'R' and resid 171 through 175 Processing helix chain 'R' and resid 226 through 231 Processing helix chain 'R' and resid 241 through 253 removed outlier: 3.580A pdb=" N THR R 253 " --> pdb=" O LEU R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 275 removed outlier: 3.554A pdb=" N LEU R 258 " --> pdb=" O ALA R 254 " (cutoff:3.500A) Proline residue: R 259 - end of helix Processing helix chain 'R' and resid 293 through 322 Proline residue: R 313 - end of helix Processing helix chain 'R' and resid 326 through 356 removed outlier: 3.693A pdb=" N TYR R 335 " --> pdb=" O TYR R 331 " (cutoff:3.500A) Proline residue: R 352 - end of helix Processing helix chain 'R' and resid 359 through 371 Processing helix chain 'C' and resid 6 through 18 Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.612A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.531A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.547A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.640A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.715A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.579A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.849A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.989A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.901A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.860A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 3.599A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.666A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 76 " --> pdb=" O HIS B 67 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.535A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 127 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.767A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 194 removed outlier: 7.373A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 208 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.877A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.769A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.748A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 91 " --> pdb=" O LEU E 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 116 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.728A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1272 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: 6.44 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8993 1.02 - 1.22: 38 1.22 - 1.41: 3822 1.41 - 1.61: 5327 1.61 - 1.81: 85 Bond restraints: 18265 Sorted by residual: bond pdb=" CA GLU R 226 " pdb=" C GLU R 226 " ideal model delta sigma weight residual 1.524 1.668 -0.144 1.32e-02 5.74e+03 1.19e+02 bond pdb=" SG CYS R 30 " pdb=" HG CYS R 30 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" N ARG R 236 " pdb=" CA ARG R 236 " ideal model delta sigma weight residual 1.455 1.389 0.066 9.60e-03 1.09e+04 4.72e+01 bond pdb=" CA ARG R 236 " pdb=" C ARG R 236 " ideal model delta sigma weight residual 1.519 1.446 0.073 1.09e-02 8.42e+03 4.43e+01 bond pdb=" C ALA R 227 " pdb=" O ALA R 227 " ideal model delta sigma weight residual 1.236 1.315 -0.080 1.32e-02 5.74e+03 3.63e+01 ... (remaining 18260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 32647 2.37 - 4.73: 190 4.73 - 7.10: 25 7.10 - 9.47: 2 9.47 - 11.83: 6 Bond angle restraints: 32870 Sorted by residual: angle pdb=" N ALA R 228 " pdb=" CA ALA R 228 " pdb=" C ALA R 228 " ideal model delta sigma weight residual 111.14 99.31 11.83 1.08e+00 8.57e-01 1.20e+02 angle pdb=" N ARG R 236 " pdb=" CA ARG R 236 " pdb=" C ARG R 236 " ideal model delta sigma weight residual 108.25 97.25 11.00 1.16e+00 7.43e-01 8.99e+01 angle pdb=" N GLU R 180 " pdb=" CA GLU R 180 " pdb=" C GLU R 180 " ideal model delta sigma weight residual 110.35 99.00 11.35 1.36e+00 5.41e-01 6.96e+01 angle pdb=" N GLN R 181 " pdb=" CA GLN R 181 " pdb=" C GLN R 181 " ideal model delta sigma weight residual 112.94 124.39 -11.45 1.41e+00 5.03e-01 6.60e+01 angle pdb=" N LEU R 230 " pdb=" CA LEU R 230 " pdb=" C LEU R 230 " ideal model delta sigma weight residual 112.34 122.44 -10.10 1.30e+00 5.92e-01 6.04e+01 ... (remaining 32865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 8259 17.66 - 35.33: 198 35.33 - 52.99: 97 52.99 - 70.65: 38 70.65 - 88.31: 7 Dihedral angle restraints: 8599 sinusoidal: 4636 harmonic: 3963 Sorted by residual: dihedral pdb=" CD ARG R 233 " pdb=" NE ARG R 233 " pdb=" CZ ARG R 233 " pdb=" NH1 ARG R 233 " ideal model delta sinusoidal sigma weight residual 0.00 -79.73 79.73 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 235 " pdb=" CB CYS R 235 " ideal model delta sinusoidal sigma weight residual 93.00 149.37 -56.37 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CA ASP R 94 " pdb=" CB ASP R 94 " pdb=" CG ASP R 94 " pdb=" OD1 ASP R 94 " ideal model delta sinusoidal sigma weight residual -30.00 -86.74 56.74 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 8596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1337 0.098 - 0.196: 73 0.196 - 0.295: 5 0.295 - 0.393: 1 0.393 - 0.491: 1 Chirality restraints: 1417 Sorted by residual: chirality pdb=" CA GLN R 181 " pdb=" N GLN R 181 " pdb=" C GLN R 181 " pdb=" CB GLN R 181 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA LEU R 230 " pdb=" N LEU R 230 " pdb=" C LEU R 230 " pdb=" CB LEU R 230 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA GLU R 226 " pdb=" N GLU R 226 " pdb=" C GLU R 226 " pdb=" CB GLU R 226 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1414 not shown) Planarity restraints: 2690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 181 " -0.099 2.00e-02 2.50e+03 4.24e-01 2.70e+03 pdb=" CD GLN R 181 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN R 181 " 0.092 2.00e-02 2.50e+03 pdb=" NE2 GLN R 181 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN R 181 " 0.722 2.00e-02 2.50e+03 pdb="HE22 GLN R 181 " -0.735 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 233 " 1.299 9.50e-02 1.11e+02 4.75e-01 1.04e+03 pdb=" NE ARG R 233 " 0.093 2.00e-02 2.50e+03 pdb=" CZ ARG R 233 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG R 233 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG R 233 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG R 233 " -0.095 2.00e-02 2.50e+03 pdb="HH12 ARG R 233 " -0.043 2.00e-02 2.50e+03 pdb="HH21 ARG R 233 " -0.399 2.00e-02 2.50e+03 pdb="HH22 ARG R 233 " 0.401 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 179 " 0.024 2.00e-02 2.50e+03 4.75e-02 2.26e+01 pdb=" C VAL R 179 " -0.082 2.00e-02 2.50e+03 pdb=" O VAL R 179 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU R 180 " 0.027 2.00e-02 2.50e+03 ... (remaining 2687 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 231 2.06 - 2.70: 28692 2.70 - 3.33: 51257 3.33 - 3.97: 65592 3.97 - 4.60: 102705 Nonbonded interactions: 248477 Sorted by model distance: nonbonded pdb=" HE ARG R 236 " pdb=" HG1 THR C 6 " model vdw 1.426 2.100 nonbonded pdb=" OD1 ASP B 158 " pdb=" H GLN B 161 " model vdw 1.639 2.450 nonbonded pdb=" OD1 ASN A 259 " pdb=" H LYS A 260 " model vdw 1.666 2.450 nonbonded pdb=" O SER R 333 " pdb="HD21 ASN R 337 " model vdw 1.667 2.450 nonbonded pdb="HH21 ARG A 205 " pdb=" OD1 ASP B 191 " model vdw 1.674 2.450 ... (remaining 248472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.320 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 40.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 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 0.144 9242 Z= 0.249 Angle : 0.548 11.834 12518 Z= 0.364 Chirality : 0.045 0.491 1417 Planarity : 0.012 0.476 1588 Dihedral : 7.468 88.314 3345 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.97 % 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: -0.45 (0.24), residues: 1128 helix: 1.15 (0.25), residues: 399 sheet: -0.39 (0.31), residues: 236 loop : -1.47 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 110 HIS 0.001 0.000 HIS B 271 PHE 0.013 0.001 PHE R 231 TYR 0.009 0.000 TYR R 96 ARG 0.007 0.000 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 355 TYR cc_start: 0.6289 (m-80) cc_final: 0.4864 (m-80) REVERT: A 188 LYS cc_start: 0.7710 (ttpp) cc_final: 0.7448 (ttpp) REVERT: A 242 SER cc_start: 0.8250 (t) cc_final: 0.7973 (p) REVERT: A 247 ARG cc_start: 0.6835 (ttm170) cc_final: 0.6587 (ttm170) REVERT: A 275 ILE cc_start: 0.8025 (mt) cc_final: 0.7615 (mt) REVERT: A 314 ASP cc_start: 0.6960 (t0) cc_final: 0.6759 (t0) REVERT: B 63 ILE cc_start: 0.7925 (mt) cc_final: 0.7672 (mt) REVERT: B 168 ASP cc_start: 0.7647 (p0) cc_final: 0.7247 (p0) REVERT: B 180 GLN cc_start: 0.6601 (mm-40) cc_final: 0.6260 (mm-40) REVERT: B 300 ASN cc_start: 0.7988 (m-40) cc_final: 0.7765 (m110) REVERT: E 42 LYS cc_start: 0.8024 (tptt) cc_final: 0.7789 (tptt) REVERT: E 88 GLU cc_start: 0.5997 (mp0) cc_final: 0.5743 (mp0) REVERT: E 115 THR cc_start: 0.8340 (t) cc_final: 0.8047 (p) REVERT: G 28 LYS cc_start: 0.7376 (mtmt) cc_final: 0.7045 (mtmt) REVERT: G 45 LYS cc_start: 0.7695 (mmtm) cc_final: 0.7309 (mmtm) outliers start: 1 outliers final: 1 residues processed: 255 average time/residue: 0.5756 time to fit residues: 191.6941 Evaluate side-chains 229 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS B 161 GLN B 225 GLN B 235 ASN E 76 ASN E 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9242 Z= 0.304 Angle : 0.581 7.381 12518 Z= 0.303 Chirality : 0.043 0.204 1417 Planarity : 0.005 0.087 1588 Dihedral : 3.961 52.907 1265 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.53 % Allowed : 7.93 % Favored : 90.54 % 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: 0.27 (0.24), residues: 1128 helix: 1.64 (0.25), residues: 410 sheet: -0.40 (0.30), residues: 268 loop : -0.75 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 337 HIS 0.007 0.002 HIS A 197 PHE 0.021 0.002 PHE R 314 TYR 0.031 0.002 TYR E 190 ARG 0.011 0.001 ARG R 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.7664 (ttpp) cc_final: 0.7337 (ttpp) REVERT: A 241 LYS cc_start: 0.7786 (tttp) cc_final: 0.7488 (ttmm) REVERT: A 247 ARG cc_start: 0.6999 (ttm170) cc_final: 0.6788 (ttm170) REVERT: A 347 LYS cc_start: 0.7818 (ttpp) cc_final: 0.7588 (ttpp) REVERT: B 259 ASP cc_start: 0.6556 (t70) cc_final: 0.6267 (t70) REVERT: B 273 ASN cc_start: 0.6779 (t0) cc_final: 0.6434 (t0) REVERT: B 339 SER cc_start: 0.7444 (m) cc_final: 0.6885 (t) REVERT: E 42 LYS cc_start: 0.8008 (tptt) cc_final: 0.7748 (tptt) REVERT: E 86 ARG cc_start: 0.7402 (mtt180) cc_final: 0.7101 (mtt180) REVERT: E 88 GLU cc_start: 0.6534 (mp0) cc_final: 0.6179 (mp0) REVERT: E 213 THR cc_start: 0.7710 (m) cc_final: 0.7344 (p) REVERT: E 215 THR cc_start: 0.7644 (m) cc_final: 0.7325 (p) REVERT: G 20 MET cc_start: 0.6722 (mmm) cc_final: 0.6389 (mmm) REVERT: G 45 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7315 (mmtm) outliers start: 15 outliers final: 13 residues processed: 262 average time/residue: 0.5844 time to fit residues: 200.1862 Evaluate side-chains 252 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 239 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 356 ASN B 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9242 Z= 0.287 Angle : 0.499 5.462 12518 Z= 0.269 Chirality : 0.041 0.161 1417 Planarity : 0.004 0.048 1588 Dihedral : 3.707 16.180 1263 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.53 % Allowed : 10.17 % Favored : 88.30 % 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: 0.62 (0.25), residues: 1128 helix: 1.96 (0.25), residues: 415 sheet: -0.31 (0.30), residues: 281 loop : -0.54 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 244 HIS 0.008 0.002 HIS E 232 PHE 0.020 0.002 PHE R 314 TYR 0.025 0.002 TYR E 190 ARG 0.006 0.001 ARG R 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7355 (ttpp) REVERT: A 241 LYS cc_start: 0.7687 (tttp) cc_final: 0.7439 (ttmm) REVERT: A 314 ASP cc_start: 0.7173 (t0) cc_final: 0.6839 (t0) REVERT: A 347 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7494 (ttpp) REVERT: B 259 ASP cc_start: 0.6654 (t70) cc_final: 0.6337 (p0) REVERT: B 273 ASN cc_start: 0.6701 (t0) cc_final: 0.6357 (t0) REVERT: B 339 SER cc_start: 0.7557 (m) cc_final: 0.7004 (t) REVERT: E 68 THR cc_start: 0.7891 (p) cc_final: 0.7677 (t) REVERT: E 86 ARG cc_start: 0.7429 (mtt180) cc_final: 0.7174 (mtt180) REVERT: E 88 GLU cc_start: 0.6718 (mp0) cc_final: 0.6365 (mp0) REVERT: E 213 THR cc_start: 0.7871 (m) cc_final: 0.7472 (p) REVERT: E 215 THR cc_start: 0.7853 (m) cc_final: 0.7482 (p) REVERT: G 20 MET cc_start: 0.6707 (mmm) cc_final: 0.6364 (mmm) REVERT: G 45 LYS cc_start: 0.7702 (mmtm) cc_final: 0.7297 (mmtm) outliers start: 15 outliers final: 11 residues processed: 238 average time/residue: 0.5923 time to fit residues: 184.0197 Evaluate side-chains 239 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 228 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 349 SER Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9242 Z= 0.283 Angle : 0.490 5.822 12518 Z= 0.259 Chirality : 0.040 0.176 1417 Planarity : 0.004 0.046 1588 Dihedral : 3.817 17.767 1263 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.83 % Allowed : 11.19 % Favored : 86.98 % 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: 0.79 (0.25), residues: 1128 helix: 2.06 (0.25), residues: 415 sheet: -0.23 (0.31), residues: 268 loop : -0.38 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.006 0.002 HIS A 324 PHE 0.019 0.001 PHE E 67 TYR 0.029 0.002 TYR E 190 ARG 0.006 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 MET cc_start: 0.5814 (tmm) cc_final: 0.5503 (tmm) REVERT: A 188 LYS cc_start: 0.7706 (ttpp) cc_final: 0.7503 (ttpp) REVERT: A 241 LYS cc_start: 0.7712 (tttp) cc_final: 0.7489 (ttmm) REVERT: A 314 ASP cc_start: 0.7093 (t0) cc_final: 0.6783 (t0) REVERT: B 259 ASP cc_start: 0.6686 (t70) cc_final: 0.6271 (p0) REVERT: B 273 ASN cc_start: 0.6701 (t0) cc_final: 0.6420 (t0) REVERT: B 339 SER cc_start: 0.7635 (m) cc_final: 0.7064 (t) REVERT: E 68 THR cc_start: 0.7939 (p) cc_final: 0.7692 (t) REVERT: E 88 GLU cc_start: 0.6808 (mp0) cc_final: 0.6457 (mp0) REVERT: E 213 THR cc_start: 0.7962 (m) cc_final: 0.7583 (p) REVERT: E 215 THR cc_start: 0.7896 (m) cc_final: 0.7417 (p) REVERT: E 238 THR cc_start: 0.8152 (m) cc_final: 0.7851 (p) REVERT: G 20 MET cc_start: 0.6772 (mmm) cc_final: 0.6391 (mmm) REVERT: G 45 LYS cc_start: 0.7670 (mmtm) cc_final: 0.7278 (mmtm) outliers start: 18 outliers final: 10 residues processed: 228 average time/residue: 0.6056 time to fit residues: 180.3415 Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 216 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9242 Z= 0.237 Angle : 0.468 5.499 12518 Z= 0.247 Chirality : 0.039 0.157 1417 Planarity : 0.004 0.047 1588 Dihedral : 3.742 18.323 1263 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.53 % Allowed : 12.21 % Favored : 86.27 % 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: 1.00 (0.25), residues: 1128 helix: 2.23 (0.25), residues: 415 sheet: -0.12 (0.32), residues: 267 loop : -0.27 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 87 HIS 0.006 0.001 HIS B 147 PHE 0.024 0.001 PHE E 67 TYR 0.025 0.001 TYR E 190 ARG 0.005 0.000 ARG R 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 MET cc_start: 0.5785 (tmm) cc_final: 0.5475 (tmm) REVERT: A 241 LYS cc_start: 0.7705 (tttp) cc_final: 0.7476 (ttmm) REVERT: A 314 ASP cc_start: 0.7063 (t0) cc_final: 0.6768 (t0) REVERT: B 259 ASP cc_start: 0.6661 (t70) cc_final: 0.6255 (p0) REVERT: B 273 ASN cc_start: 0.6691 (t0) cc_final: 0.6399 (t0) REVERT: B 339 SER cc_start: 0.7624 (m) cc_final: 0.7046 (t) REVERT: E 68 THR cc_start: 0.7958 (p) cc_final: 0.7692 (t) REVERT: E 88 GLU cc_start: 0.6810 (mp0) cc_final: 0.6451 (mp0) REVERT: E 115 THR cc_start: 0.8377 (t) cc_final: 0.7929 (p) REVERT: E 213 THR cc_start: 0.8016 (m) cc_final: 0.7637 (p) REVERT: E 238 THR cc_start: 0.8145 (m) cc_final: 0.7833 (p) REVERT: G 20 MET cc_start: 0.6765 (mmm) cc_final: 0.6398 (mmm) REVERT: G 45 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7274 (mmtm) outliers start: 15 outliers final: 12 residues processed: 227 average time/residue: 0.5990 time to fit residues: 177.2093 Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9242 Z= 0.362 Angle : 0.516 6.113 12518 Z= 0.275 Chirality : 0.041 0.181 1417 Planarity : 0.004 0.050 1588 Dihedral : 4.003 18.931 1263 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.42 % Allowed : 13.02 % Favored : 85.55 % 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: 0.98 (0.25), residues: 1128 helix: 2.11 (0.25), residues: 415 sheet: -0.00 (0.32), residues: 260 loop : -0.27 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 216 HIS 0.006 0.002 HIS B 147 PHE 0.020 0.002 PHE R 314 TYR 0.032 0.002 TYR E 190 ARG 0.005 0.000 ARG R 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 248 MET cc_start: 0.5785 (tmm) cc_final: 0.5457 (tmm) REVERT: A 241 LYS cc_start: 0.7689 (tttp) cc_final: 0.7470 (ttmm) REVERT: A 314 ASP cc_start: 0.7014 (t0) cc_final: 0.6743 (t0) REVERT: B 196 SER cc_start: 0.8344 (t) cc_final: 0.8113 (m) REVERT: B 273 ASN cc_start: 0.6743 (t0) cc_final: 0.6453 (t0) REVERT: B 339 SER cc_start: 0.7756 (m) cc_final: 0.7304 (p) REVERT: E 88 GLU cc_start: 0.6886 (mp0) cc_final: 0.6552 (mp0) REVERT: E 108 ASP cc_start: 0.7479 (p0) cc_final: 0.7241 (p0) REVERT: E 115 THR cc_start: 0.8368 (t) cc_final: 0.7914 (p) REVERT: E 213 THR cc_start: 0.8094 (m) cc_final: 0.7708 (p) REVERT: E 238 THR cc_start: 0.8138 (m) cc_final: 0.7750 (p) REVERT: G 20 MET cc_start: 0.6848 (mmm) cc_final: 0.6475 (mmm) REVERT: G 45 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7287 (mmtm) outliers start: 14 outliers final: 12 residues processed: 226 average time/residue: 0.6486 time to fit residues: 189.8354 Evaluate side-chains 227 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 54 SER Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 299 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9242 Z= 0.181 Angle : 0.456 5.115 12518 Z= 0.240 Chirality : 0.039 0.157 1417 Planarity : 0.004 0.044 1588 Dihedral : 3.776 18.241 1263 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.42 % Allowed : 13.53 % Favored : 85.05 % 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: 1.21 (0.26), residues: 1128 helix: 2.44 (0.26), residues: 415 sheet: 0.06 (0.32), residues: 259 loop : -0.24 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.005 0.001 HIS A 324 PHE 0.018 0.001 PHE E 67 TYR 0.021 0.001 TYR E 190 ARG 0.006 0.000 ARG R 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASP cc_start: 0.6297 (t70) cc_final: 0.5987 (t0) REVERT: A 241 LYS cc_start: 0.7698 (tttp) cc_final: 0.7472 (ttmm) REVERT: A 260 LYS cc_start: 0.8220 (mttm) cc_final: 0.7985 (mttt) REVERT: A 314 ASP cc_start: 0.7008 (t0) cc_final: 0.6719 (t0) REVERT: B 160 ASN cc_start: 0.7936 (t0) cc_final: 0.7476 (t0) REVERT: B 248 THR cc_start: 0.7441 (p) cc_final: 0.7231 (p) REVERT: B 273 ASN cc_start: 0.6685 (t0) cc_final: 0.6399 (t0) REVERT: B 339 SER cc_start: 0.7629 (m) cc_final: 0.7037 (t) REVERT: E 88 GLU cc_start: 0.6848 (mp0) cc_final: 0.6506 (mp0) REVERT: E 213 THR cc_start: 0.8067 (m) cc_final: 0.7694 (p) REVERT: E 238 THR cc_start: 0.8119 (m) cc_final: 0.7736 (p) REVERT: G 20 MET cc_start: 0.6821 (mmm) cc_final: 0.6427 (mmm) REVERT: G 45 LYS cc_start: 0.7656 (mmtm) cc_final: 0.7266 (mmtm) outliers start: 14 outliers final: 11 residues processed: 225 average time/residue: 0.6260 time to fit residues: 182.6152 Evaluate side-chains 224 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9242 Z= 0.232 Angle : 0.476 5.264 12518 Z= 0.251 Chirality : 0.039 0.154 1417 Planarity : 0.004 0.047 1588 Dihedral : 3.782 17.718 1263 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.12 % Allowed : 14.65 % Favored : 84.23 % 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: 1.20 (0.26), residues: 1128 helix: 2.45 (0.26), residues: 415 sheet: 0.07 (0.32), residues: 253 loop : -0.27 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 87 HIS 0.020 0.002 HIS A 324 PHE 0.016 0.001 PHE R 314 TYR 0.024 0.001 TYR E 190 ARG 0.006 0.000 ARG R 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 216 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASP cc_start: 0.6324 (t70) cc_final: 0.6017 (t0) REVERT: A 226 ASP cc_start: 0.7487 (t0) cc_final: 0.7281 (t70) REVERT: A 241 LYS cc_start: 0.7659 (tttp) cc_final: 0.7440 (ttmm) REVERT: A 260 LYS cc_start: 0.8211 (mttm) cc_final: 0.7937 (mttt) REVERT: A 314 ASP cc_start: 0.7032 (t0) cc_final: 0.6735 (t0) REVERT: B 160 ASN cc_start: 0.7896 (t0) cc_final: 0.7472 (t0) REVERT: B 248 THR cc_start: 0.7437 (p) cc_final: 0.7229 (p) REVERT: B 273 ASN cc_start: 0.6683 (t0) cc_final: 0.6395 (t0) REVERT: B 339 SER cc_start: 0.7672 (m) cc_final: 0.7064 (t) REVERT: E 213 THR cc_start: 0.8103 (m) cc_final: 0.7732 (p) REVERT: E 215 THR cc_start: 0.7992 (m) cc_final: 0.7512 (p) REVERT: E 238 THR cc_start: 0.8108 (m) cc_final: 0.7729 (p) REVERT: G 20 MET cc_start: 0.6825 (mmm) cc_final: 0.6447 (mmm) REVERT: G 45 LYS cc_start: 0.7656 (mmtm) cc_final: 0.7267 (mmtm) outliers start: 11 outliers final: 9 residues processed: 222 average time/residue: 0.6375 time to fit residues: 182.3539 Evaluate side-chains 223 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 347 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9242 Z= 0.251 Angle : 0.481 5.401 12518 Z= 0.253 Chirality : 0.039 0.153 1417 Planarity : 0.004 0.046 1588 Dihedral : 3.847 17.753 1263 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.42 % Allowed : 14.14 % Favored : 84.44 % 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: 1.21 (0.26), residues: 1128 helix: 2.43 (0.26), residues: 415 sheet: 0.04 (0.32), residues: 259 loop : -0.22 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 87 HIS 0.014 0.002 HIS A 324 PHE 0.018 0.001 PHE E 67 TYR 0.025 0.001 TYR E 190 ARG 0.006 0.000 ARG R 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASP cc_start: 0.6352 (t70) cc_final: 0.6029 (t0) REVERT: A 241 LYS cc_start: 0.7688 (tttp) cc_final: 0.7472 (ttmm) REVERT: A 314 ASP cc_start: 0.7004 (t0) cc_final: 0.6709 (t0) REVERT: A 323 ARG cc_start: 0.6487 (OUTLIER) cc_final: 0.6277 (ptt90) REVERT: B 196 SER cc_start: 0.8368 (t) cc_final: 0.8159 (m) REVERT: B 248 THR cc_start: 0.7465 (p) cc_final: 0.7257 (p) REVERT: B 259 ASP cc_start: 0.6566 (t70) cc_final: 0.6330 (p0) REVERT: B 273 ASN cc_start: 0.6676 (t0) cc_final: 0.6377 (t0) REVERT: B 339 SER cc_start: 0.7675 (m) cc_final: 0.7179 (p) REVERT: E 213 THR cc_start: 0.8119 (m) cc_final: 0.7758 (p) REVERT: E 215 THR cc_start: 0.8006 (m) cc_final: 0.7534 (p) REVERT: E 238 THR cc_start: 0.8107 (m) cc_final: 0.7703 (p) REVERT: G 20 MET cc_start: 0.6783 (mmm) cc_final: 0.6417 (mmm) REVERT: G 45 LYS cc_start: 0.7679 (mmtm) cc_final: 0.7292 (mmtm) outliers start: 14 outliers final: 11 residues processed: 222 average time/residue: 0.6253 time to fit residues: 179.3732 Evaluate side-chains 228 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain R residue 347 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.0980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9242 Z= 0.210 Angle : 0.469 5.190 12518 Z= 0.247 Chirality : 0.039 0.155 1417 Planarity : 0.004 0.045 1588 Dihedral : 3.771 17.324 1263 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.12 % Allowed : 14.65 % Favored : 84.23 % 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: 1.30 (0.26), residues: 1128 helix: 2.55 (0.26), residues: 415 sheet: 0.07 (0.32), residues: 260 loop : -0.20 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.007 0.001 HIS A 324 PHE 0.017 0.001 PHE R 314 TYR 0.021 0.001 TYR E 190 ARG 0.007 0.000 ARG R 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASP cc_start: 0.6328 (t70) cc_final: 0.6004 (t0) REVERT: A 241 LYS cc_start: 0.7652 (tttp) cc_final: 0.7438 (ttmm) REVERT: A 260 LYS cc_start: 0.8209 (mttm) cc_final: 0.7975 (mttp) REVERT: A 314 ASP cc_start: 0.7009 (t0) cc_final: 0.6703 (t0) REVERT: A 323 ARG cc_start: 0.6546 (OUTLIER) cc_final: 0.6319 (ptt90) REVERT: B 259 ASP cc_start: 0.6559 (t70) cc_final: 0.6336 (p0) REVERT: B 273 ASN cc_start: 0.6669 (t0) cc_final: 0.6376 (t0) REVERT: B 332 VAL cc_start: 0.8222 (t) cc_final: 0.7901 (p) REVERT: B 339 SER cc_start: 0.7657 (m) cc_final: 0.7166 (p) REVERT: E 213 THR cc_start: 0.8107 (m) cc_final: 0.7750 (p) REVERT: G 20 MET cc_start: 0.6759 (mmm) cc_final: 0.6394 (mmm) REVERT: G 45 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7292 (mmtm) outliers start: 11 outliers final: 8 residues processed: 219 average time/residue: 0.6426 time to fit residues: 182.4665 Evaluate side-chains 223 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 341 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 ARG Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 72 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.138852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118144 restraints weight = 34384.105| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.78 r_work: 0.3313 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9242 Z= 0.402 Angle : 0.541 6.194 12518 Z= 0.287 Chirality : 0.042 0.177 1417 Planarity : 0.004 0.053 1588 Dihedral : 4.131 18.181 1263 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.22 % Allowed : 14.24 % Favored : 84.54 % 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: 1.01 (0.25), residues: 1128 helix: 2.18 (0.25), residues: 415 sheet: 0.02 (0.32), residues: 270 loop : -0.29 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 216 HIS 0.009 0.002 HIS A 324 PHE 0.016 0.002 PHE R 344 TYR 0.032 0.002 TYR E 190 ARG 0.008 0.000 ARG R 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5479.07 seconds wall clock time: 97 minutes 56.24 seconds (5876.24 seconds total)