Starting phenix.real_space_refine on Fri Oct 11 03:38:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xwq_38741/10_2024/8xwq_38741.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xwq_38741/10_2024/8xwq_38741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xwq_38741/10_2024/8xwq_38741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xwq_38741/10_2024/8xwq_38741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xwq_38741/10_2024/8xwq_38741.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xwq_38741/10_2024/8xwq_38741.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 70 5.16 5 C 5795 2.51 5 N 1527 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9076 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2404 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.35, per 1000 atoms: 0.59 Number of scatterers: 9076 At special positions: 0 Unit cell: (120.34, 126.904, 109.4, 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 70 16.00 O 1684 8.00 N 1527 7.00 C 5795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " 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: 2.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.633A pdb=" N VAL R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 162 Proline residue: R 156 - end of helix removed outlier: 3.729A pdb=" N LEU R 162 " --> pdb=" O ASN R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 205 Proline residue: R 178 - end of helix removed outlier: 4.603A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 238 removed outlier: 3.752A pdb=" N VAL R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) Proline residue: R 235 - end of helix removed outlier: 3.611A pdb=" N ILE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 removed outlier: 4.154A pdb=" N ALA R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 282 removed outlier: 3.675A pdb=" N TRP R 276 " --> pdb=" O ALA R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 Processing helix chain 'R' and resid 313 through 349 Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 356 through 388 removed outlier: 3.745A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 398 Processing helix chain 'L' and resid 10 through 18 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.676A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.553A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.651A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.742A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 243 Processing sheet with id=AA2, first strand: chain 'R' and resid 246 through 247 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.630A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.722A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.132A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.778A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.656A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.134A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.856A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.588A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.478A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.429A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1269 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: 2.84 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2906 1.35 - 1.47: 2282 1.47 - 1.59: 3980 1.59 - 1.71: 0 1.71 - 1.83: 98 Bond restraints: 9266 Sorted by residual: bond pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.21e-02 6.83e+03 2.19e+00 bond pdb=" CA LYS L 9 " pdb=" C LYS L 9 " ideal model delta sigma weight residual 1.522 1.504 0.018 1.38e-02 5.25e+03 1.67e+00 bond pdb=" CA VAL R 234 " pdb=" C VAL R 234 " ideal model delta sigma weight residual 1.520 1.530 -0.010 8.80e-03 1.29e+04 1.34e+00 bond pdb=" CB ARG R 208 " pdb=" CG ARG R 208 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CA ALA B 92 " pdb=" C ALA B 92 " ideal model delta sigma weight residual 1.528 1.518 0.010 1.18e-02 7.18e+03 7.90e-01 ... (remaining 9261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 12053 1.22 - 2.43: 419 2.43 - 3.65: 66 3.65 - 4.87: 11 4.87 - 6.08: 5 Bond angle restraints: 12554 Sorted by residual: angle pdb=" C VAL R 234 " pdb=" CA VAL R 234 " pdb=" CB VAL R 234 " ideal model delta sigma weight residual 114.35 109.69 4.66 1.06e+00 8.90e-01 1.94e+01 angle pdb=" N MET L 7 " pdb=" CA MET L 7 " pdb=" C MET L 7 " ideal model delta sigma weight residual 114.39 110.35 4.04 1.45e+00 4.76e-01 7.77e+00 angle pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " pdb=" CG ARG R 208 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.13e+00 angle pdb=" C ALA R 233 " pdb=" N VAL R 234 " pdb=" CA VAL R 234 " ideal model delta sigma weight residual 120.24 121.90 -1.66 6.30e-01 2.52e+00 6.94e+00 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.22e+00 ... (remaining 12549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5086 17.60 - 35.19: 325 35.19 - 52.79: 89 52.79 - 70.38: 14 70.38 - 87.98: 2 Dihedral angle restraints: 5516 sinusoidal: 2140 harmonic: 3376 Sorted by residual: dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 255 " pdb=" CB CYS R 255 " ideal model delta sinusoidal sigma weight residual -86.00 -126.43 40.43 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CA LEU R 256 " pdb=" C LEU R 256 " pdb=" N LEU R 257 " pdb=" CA LEU R 257 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ARG A 208 " pdb=" C ARG A 208 " pdb=" N LYS A 209 " pdb=" CA LYS A 209 " ideal model delta harmonic sigma weight residual -180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 871 0.026 - 0.053: 339 0.053 - 0.079: 128 0.079 - 0.106: 70 0.106 - 0.132: 24 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CA ILE D 51 " pdb=" N ILE D 51 " pdb=" C ILE D 51 " pdb=" CB ILE D 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA PRO R 338 " pdb=" N PRO R 338 " pdb=" C PRO R 338 " pdb=" CB PRO R 338 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE D 145 " pdb=" N ILE D 145 " pdb=" C ILE D 145 " pdb=" CB ILE D 145 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1429 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 370 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C ILE R 370 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE R 370 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY R 371 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 369 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00 pdb=" C TYR R 369 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR R 369 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE R 370 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 279 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C SER R 279 " -0.025 2.00e-02 2.50e+03 pdb=" O SER R 279 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE R 280 " 0.008 2.00e-02 2.50e+03 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 304 2.70 - 3.25: 9489 3.25 - 3.80: 15106 3.80 - 4.35: 18987 4.35 - 4.90: 31340 Nonbonded interactions: 75226 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.145 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.174 3.040 nonbonded pdb=" OE2 GLU R 236 " pdb=" OH TYR R 269 " model vdw 2.191 3.040 nonbonded pdb=" O GLU R 359 " pdb=" OG SER R 362 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.217 3.040 ... (remaining 75221 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 23.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9266 Z= 0.172 Angle : 0.546 6.083 12554 Z= 0.323 Chirality : 0.038 0.132 1432 Planarity : 0.003 0.036 1579 Dihedral : 12.776 87.977 3318 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 7.98 % Allowed : 9.19 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.12 (0.25), residues: 1143 helix: 1.47 (0.27), residues: 413 sheet: -0.12 (0.35), residues: 228 loop : -1.40 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 336 HIS 0.003 0.001 HIS B 266 PHE 0.014 0.001 PHE R 291 TYR 0.009 0.001 TYR D 223 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 425 time to evaluate : 1.122 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: 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 94 ILE cc_start: 0.8348 (mt) cc_final: 0.6448 (pt) REVERT: R 126 ILE cc_start: 0.8485 (mp) cc_final: 0.8267 (mp) REVERT: R 134 ASN cc_start: 0.7224 (p0) cc_final: 0.6938 (t0) REVERT: R 138 ILE cc_start: 0.8766 (mt) cc_final: 0.8507 (pt) REVERT: R 175 LYS cc_start: 0.7442 (tttp) cc_final: 0.6965 (pttt) REVERT: R 190 LEU cc_start: 0.9594 (mt) cc_final: 0.9379 (mt) REVERT: R 236 GLU cc_start: 0.8157 (mp0) cc_final: 0.7310 (mp0) REVERT: R 240 PHE cc_start: 0.8987 (m-80) cc_final: 0.8201 (m-80) REVERT: R 280 PHE cc_start: 0.8633 (t80) cc_final: 0.8129 (m-10) REVERT: R 293 TYR cc_start: 0.8758 (m-10) cc_final: 0.8526 (m-10) REVERT: R 295 LEU cc_start: 0.9002 (mt) cc_final: 0.8802 (mt) REVERT: R 313 ASP cc_start: 0.8472 (t70) cc_final: 0.8260 (t70) REVERT: R 319 ARG cc_start: 0.7525 (mtt180) cc_final: 0.7059 (tmt170) REVERT: R 323 LYS cc_start: 0.5326 (OUTLIER) cc_final: 0.5108 (pttt) REVERT: R 326 PHE cc_start: 0.8362 (m-10) cc_final: 0.7704 (t80) REVERT: R 327 CYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8459 (t) REVERT: R 336 TRP cc_start: 0.8793 (m100) cc_final: 0.8519 (m100) REVERT: R 370 ILE cc_start: 0.9045 (mm) cc_final: 0.8651 (tt) REVERT: L 8 ASP cc_start: 0.4458 (OUTLIER) cc_final: 0.3732 (p0) REVERT: L 10 GLU cc_start: 0.8476 (mp0) cc_final: 0.8112 (pm20) REVERT: A 21 ARG cc_start: 0.8954 (mtm110) cc_final: 0.8592 (ptm160) REVERT: A 43 GLU cc_start: 0.6963 (pm20) cc_final: 0.5885 (tt0) REVERT: A 213 HIS cc_start: 0.8726 (p90) cc_final: 0.7710 (p90) REVERT: A 215 PHE cc_start: 0.8907 (m-80) cc_final: 0.8705 (m-80) REVERT: A 216 GLU cc_start: 0.8803 (tt0) cc_final: 0.8313 (tp30) REVERT: A 224 CYS cc_start: 0.9306 (m) cc_final: 0.7989 (t) REVERT: A 230 TYR cc_start: 0.5349 (OUTLIER) cc_final: 0.4792 (p90) REVERT: A 242 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8029 (mmp-170) REVERT: A 250 PHE cc_start: 0.9485 (t80) cc_final: 0.9023 (t80) REVERT: A 256 ASN cc_start: 0.9127 (m-40) cc_final: 0.8829 (t0) REVERT: A 269 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8517 (p0) REVERT: A 298 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8735 (pp20) REVERT: A 304 GLN cc_start: 0.9405 (tt0) cc_final: 0.9114 (tm-30) REVERT: A 320 TYR cc_start: 0.8764 (m-80) cc_final: 0.7256 (m-80) REVERT: A 348 LEU cc_start: 0.9593 (mt) cc_final: 0.9101 (tp) REVERT: A 349 LYS cc_start: 0.9402 (ttmm) cc_final: 0.9182 (mtmm) REVERT: B 45 MET cc_start: 0.8663 (mmm) cc_final: 0.8282 (mmm) REVERT: B 57 LYS cc_start: 0.9067 (pttp) cc_final: 0.8465 (ptpt) REVERT: B 59 TYR cc_start: 0.8001 (m-80) cc_final: 0.7097 (m-80) REVERT: B 63 TRP cc_start: 0.9314 (m100) cc_final: 0.8928 (m100) REVERT: B 81 ILE cc_start: 0.9529 (mt) cc_final: 0.9225 (tp) REVERT: B 89 LYS cc_start: 0.8889 (mptt) cc_final: 0.8529 (mmtp) REVERT: B 119 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8208 (m-40) REVERT: B 146 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8063 (tp) REVERT: B 157 ILE cc_start: 0.9489 (tt) cc_final: 0.9187 (tt) REVERT: B 180 PHE cc_start: 0.8319 (m-80) cc_final: 0.7891 (m-80) REVERT: B 192 LEU cc_start: 0.8573 (mt) cc_final: 0.8076 (pt) REVERT: B 222 PHE cc_start: 0.8236 (m-80) cc_final: 0.7955 (m-80) REVERT: B 234 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7977 (t80) REVERT: B 243 THR cc_start: 0.8301 (p) cc_final: 0.8062 (t) REVERT: B 267 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8651 (p0) REVERT: B 278 PHE cc_start: 0.8340 (m-80) cc_final: 0.8108 (m-80) REVERT: B 283 ARG cc_start: 0.8593 (tpt90) cc_final: 0.8339 (tpt170) REVERT: B 289 TYR cc_start: 0.8087 (m-80) cc_final: 0.6525 (m-80) REVERT: B 335 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.5704 (m-10) REVERT: C 24 ASN cc_start: 0.9216 (t0) cc_final: 0.8783 (p0) REVERT: C 36 ASP cc_start: 0.9132 (m-30) cc_final: 0.8891 (m-30) REVERT: D 35 HIS cc_start: 0.9054 (m-70) cc_final: 0.8486 (m-70) REVERT: D 36 TRP cc_start: 0.8295 (m100) cc_final: 0.7440 (m100) REVERT: D 73 ASP cc_start: 0.8855 (t70) cc_final: 0.8636 (t0) REVERT: D 74 ASP cc_start: 0.9082 (m-30) cc_final: 0.8808 (m-30) REVERT: D 77 ASN cc_start: 0.8784 (m-40) cc_final: 0.8424 (p0) REVERT: D 78 THR cc_start: 0.9066 (m) cc_final: 0.8624 (p) REVERT: D 79 LEU cc_start: 0.9500 (tp) cc_final: 0.9213 (tp) REVERT: D 108 PHE cc_start: 0.9011 (m-80) cc_final: 0.8763 (m-80) REVERT: D 111 TRP cc_start: 0.8265 (m100) cc_final: 0.7502 (m-10) REVERT: D 165 PHE cc_start: 0.9072 (m-80) cc_final: 0.8729 (m-80) outliers start: 79 outliers final: 24 residues processed: 470 average time/residue: 0.2470 time to fit residues: 151.8604 Evaluate side-chains 311 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 276 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS R 181 GLN R 258 HIS R 317 GLN A 188 HIS A 195 HIS A 244 HIS A 294 ASN A 304 GLN B 32 GLN B 156 GLN B 268 ASN D 167 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9266 Z= 0.226 Angle : 0.648 7.683 12554 Z= 0.347 Chirality : 0.044 0.223 1432 Planarity : 0.005 0.054 1579 Dihedral : 4.669 30.178 1251 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.20 % Allowed : 4.14 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.17 (0.25), residues: 1143 helix: 1.26 (0.25), residues: 401 sheet: -0.23 (0.33), residues: 239 loop : -1.17 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 36 HIS 0.013 0.002 HIS B 225 PHE 0.016 0.002 PHE R 397 TYR 0.019 0.002 TYR D 161 ARG 0.007 0.001 ARG R 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 348 time to evaluate : 1.083 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 ILE cc_start: 0.8144 (mt) cc_final: 0.7697 (mp) REVERT: R 134 ASN cc_start: 0.7040 (p0) cc_final: 0.6400 (t0) REVERT: R 257 LEU cc_start: 0.8954 (mm) cc_final: 0.8640 (mm) REVERT: R 280 PHE cc_start: 0.8525 (t80) cc_final: 0.7845 (m-80) REVERT: R 326 PHE cc_start: 0.8307 (m-10) cc_final: 0.7657 (t80) REVERT: L 7 MET cc_start: 0.7754 (tmm) cc_final: 0.7425 (tmm) REVERT: L 10 GLU cc_start: 0.8342 (mp0) cc_final: 0.7913 (pm20) REVERT: L 13 TYR cc_start: 0.8190 (t80) cc_final: 0.7803 (t80) REVERT: A 5 LEU cc_start: 0.7806 (mt) cc_final: 0.7553 (pt) REVERT: A 24 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7406 (mmm-85) REVERT: A 188 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.8076 (t-90) REVERT: A 213 HIS cc_start: 0.8673 (p90) cc_final: 0.7585 (p90) REVERT: A 216 GLU cc_start: 0.8799 (tt0) cc_final: 0.8314 (tp30) REVERT: A 223 PHE cc_start: 0.8723 (t80) cc_final: 0.8430 (t80) REVERT: A 224 CYS cc_start: 0.9181 (m) cc_final: 0.7639 (t) REVERT: A 243 MET cc_start: 0.9216 (ttp) cc_final: 0.8410 (tmm) REVERT: A 247 MET cc_start: 0.9191 (mtm) cc_final: 0.8326 (mtm) REVERT: A 248 LYS cc_start: 0.9313 (mtmm) cc_final: 0.9084 (mttt) REVERT: A 256 ASN cc_start: 0.9066 (m-40) cc_final: 0.8839 (m110) REVERT: A 269 ASN cc_start: 0.9135 (m110) cc_final: 0.7583 (m-40) REVERT: A 304 GLN cc_start: 0.9429 (tt0) cc_final: 0.9141 (tm-30) REVERT: A 317 LYS cc_start: 0.8380 (pttt) cc_final: 0.8153 (pttp) REVERT: A 348 LEU cc_start: 0.9475 (mt) cc_final: 0.9164 (tp) REVERT: B 51 LEU cc_start: 0.9044 (mp) cc_final: 0.8606 (tp) REVERT: B 57 LYS cc_start: 0.9038 (pttp) cc_final: 0.8721 (ptpt) REVERT: B 63 TRP cc_start: 0.9353 (m100) cc_final: 0.9040 (m100) REVERT: B 69 LEU cc_start: 0.9525 (mt) cc_final: 0.8695 (pp) REVERT: B 146 LEU cc_start: 0.7447 (mp) cc_final: 0.6978 (mp) REVERT: B 180 PHE cc_start: 0.8427 (m-80) cc_final: 0.8017 (m-80) REVERT: B 192 LEU cc_start: 0.8508 (mt) cc_final: 0.8092 (pt) REVERT: B 222 PHE cc_start: 0.8230 (m-80) cc_final: 0.8028 (m-80) REVERT: B 254 ASP cc_start: 0.7483 (t70) cc_final: 0.7268 (t0) REVERT: B 283 ARG cc_start: 0.9060 (tpt90) cc_final: 0.8846 (tpt170) REVERT: B 289 TYR cc_start: 0.7886 (m-80) cc_final: 0.6396 (m-80) REVERT: C 24 ASN cc_start: 0.8957 (t0) cc_final: 0.8548 (p0) REVERT: D 35 HIS cc_start: 0.8908 (m-70) cc_final: 0.8340 (m-70) REVERT: D 46 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8713 (mm-30) REVERT: D 73 ASP cc_start: 0.9078 (t70) cc_final: 0.8575 (t0) REVERT: D 78 THR cc_start: 0.9150 (m) cc_final: 0.8728 (p) REVERT: D 89 GLU cc_start: 0.8818 (mp0) cc_final: 0.8297 (pm20) REVERT: D 111 TRP cc_start: 0.8355 (m100) cc_final: 0.7800 (m-10) REVERT: D 145 ILE cc_start: 0.8604 (pt) cc_final: 0.8334 (pt) REVERT: D 164 TRP cc_start: 0.8153 (m100) cc_final: 0.7414 (m-10) REVERT: D 165 PHE cc_start: 0.8949 (m-80) cc_final: 0.8583 (m-80) REVERT: D 202 LEU cc_start: 0.9199 (tt) cc_final: 0.8533 (tt) outliers start: 2 outliers final: 1 residues processed: 348 average time/residue: 0.2340 time to fit residues: 108.6564 Evaluate side-chains 259 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 257 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 103 optimal weight: 0.0970 chunk 112 optimal weight: 0.0270 chunk 92 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.1038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 119 ASN R 150 HIS R 181 GLN R 258 HIS A 195 HIS B 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9266 Z= 0.191 Angle : 0.619 9.023 12554 Z= 0.321 Chirality : 0.043 0.181 1432 Planarity : 0.004 0.043 1579 Dihedral : 4.579 31.943 1251 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.30 % Allowed : 4.14 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.25), residues: 1143 helix: 1.16 (0.26), residues: 402 sheet: -0.21 (0.33), residues: 239 loop : -1.12 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 336 HIS 0.006 0.001 HIS R 150 PHE 0.026 0.002 PHE D 68 TYR 0.013 0.001 TYR R 251 ARG 0.006 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 326 time to evaluate : 1.093 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 ILE cc_start: 0.8086 (mt) cc_final: 0.7386 (mp) REVERT: R 190 LEU cc_start: 0.9535 (mt) cc_final: 0.9325 (mt) REVERT: R 245 MET cc_start: 0.9023 (mpp) cc_final: 0.8620 (mpp) REVERT: R 280 PHE cc_start: 0.8471 (t80) cc_final: 0.7895 (m-80) REVERT: R 293 TYR cc_start: 0.8533 (m-10) cc_final: 0.8275 (m-80) REVERT: R 320 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8403 (mt-10) REVERT: R 326 PHE cc_start: 0.8392 (m-10) cc_final: 0.7631 (t80) REVERT: R 339 LEU cc_start: 0.9456 (pt) cc_final: 0.9212 (pp) REVERT: L 7 MET cc_start: 0.7699 (tmm) cc_final: 0.7260 (tmm) REVERT: L 10 GLU cc_start: 0.8403 (mp0) cc_final: 0.7929 (pm20) REVERT: L 13 TYR cc_start: 0.8282 (t80) cc_final: 0.7843 (t80) REVERT: A 5 LEU cc_start: 0.7736 (mt) cc_final: 0.7274 (pt) REVERT: A 24 ARG cc_start: 0.7895 (mtt180) cc_final: 0.7368 (mmm-85) REVERT: A 196 PHE cc_start: 0.9100 (m-10) cc_final: 0.8869 (m-10) REVERT: A 213 HIS cc_start: 0.8714 (p90) cc_final: 0.7741 (p90) REVERT: A 216 GLU cc_start: 0.8745 (tt0) cc_final: 0.8214 (tp30) REVERT: A 223 PHE cc_start: 0.8726 (t80) cc_final: 0.8201 (t80) REVERT: A 224 CYS cc_start: 0.9281 (m) cc_final: 0.7683 (t) REVERT: A 243 MET cc_start: 0.8988 (ttp) cc_final: 0.8467 (tmm) REVERT: A 247 MET cc_start: 0.9168 (mtm) cc_final: 0.8538 (mtm) REVERT: A 248 LYS cc_start: 0.9316 (mtmm) cc_final: 0.9084 (mttt) REVERT: A 256 ASN cc_start: 0.9078 (m-40) cc_final: 0.8814 (m110) REVERT: A 269 ASN cc_start: 0.9121 (m110) cc_final: 0.7534 (m-40) REVERT: A 304 GLN cc_start: 0.9396 (tt0) cc_final: 0.9099 (tm-30) REVERT: B 49 ARG cc_start: 0.8735 (mmt180) cc_final: 0.8383 (mmt90) REVERT: B 51 LEU cc_start: 0.9010 (mp) cc_final: 0.8661 (tp) REVERT: B 69 LEU cc_start: 0.9498 (mt) cc_final: 0.8641 (pp) REVERT: B 101 MET cc_start: 0.8704 (mtm) cc_final: 0.7573 (mtm) REVERT: B 114 CYS cc_start: 0.8356 (t) cc_final: 0.8151 (t) REVERT: B 127 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8786 (mttp) REVERT: B 146 LEU cc_start: 0.7815 (mp) cc_final: 0.7286 (mp) REVERT: B 180 PHE cc_start: 0.8475 (m-80) cc_final: 0.6839 (m-80) REVERT: B 192 LEU cc_start: 0.8527 (mt) cc_final: 0.8168 (pt) REVERT: B 219 ARG cc_start: 0.8199 (tpt90) cc_final: 0.7966 (tpt90) REVERT: B 222 PHE cc_start: 0.8156 (m-80) cc_final: 0.7729 (m-80) REVERT: B 254 ASP cc_start: 0.7647 (t70) cc_final: 0.7418 (t0) REVERT: B 283 ARG cc_start: 0.8968 (tpt90) cc_final: 0.8703 (tpt170) REVERT: B 289 TYR cc_start: 0.7689 (m-80) cc_final: 0.6250 (m-80) REVERT: C 17 GLU cc_start: 0.9165 (pt0) cc_final: 0.8962 (pt0) REVERT: C 21 MET cc_start: 0.8837 (mmp) cc_final: 0.8505 (mmm) REVERT: D 45 LEU cc_start: 0.9414 (mt) cc_final: 0.8780 (mt) REVERT: D 73 ASP cc_start: 0.9022 (t70) cc_final: 0.8720 (t0) REVERT: D 78 THR cc_start: 0.9062 (m) cc_final: 0.8391 (p) REVERT: D 80 PHE cc_start: 0.8753 (m-80) cc_final: 0.8429 (m-10) REVERT: D 111 TRP cc_start: 0.8298 (m100) cc_final: 0.7843 (m-10) REVERT: D 159 ASN cc_start: 0.9233 (m110) cc_final: 0.8871 (t0) REVERT: D 164 TRP cc_start: 0.8082 (m100) cc_final: 0.7118 (m-10) REVERT: D 202 LEU cc_start: 0.9233 (tt) cc_final: 0.8573 (tt) REVERT: D 227 PHE cc_start: 0.8368 (m-80) cc_final: 0.8153 (m-10) outliers start: 3 outliers final: 0 residues processed: 327 average time/residue: 0.2254 time to fit residues: 99.5055 Evaluate side-chains 245 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 0.0040 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS R 181 GLN A 188 HIS A 195 HIS A 294 ASN B 32 GLN D 35 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9266 Z= 0.190 Angle : 0.604 7.257 12554 Z= 0.316 Chirality : 0.043 0.147 1432 Planarity : 0.004 0.043 1579 Dihedral : 4.583 32.536 1251 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.20 % Allowed : 4.55 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.25 (0.25), residues: 1143 helix: 0.99 (0.25), residues: 401 sheet: -0.21 (0.33), residues: 239 loop : -1.06 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 36 HIS 0.007 0.001 HIS B 225 PHE 0.023 0.001 PHE B 278 TYR 0.013 0.002 TYR B 145 ARG 0.008 0.001 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 313 time to evaluate : 1.111 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 ILE cc_start: 0.7948 (mt) cc_final: 0.7190 (mp) REVERT: R 132 MET cc_start: 0.6131 (ttt) cc_final: 0.5662 (ttt) REVERT: R 190 LEU cc_start: 0.9544 (mt) cc_final: 0.9330 (mt) REVERT: R 245 MET cc_start: 0.8955 (mpp) cc_final: 0.8624 (mpp) REVERT: R 280 PHE cc_start: 0.8458 (t80) cc_final: 0.7793 (m-80) REVERT: R 320 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8352 (mt-10) REVERT: R 326 PHE cc_start: 0.8303 (m-10) cc_final: 0.7677 (t80) REVERT: L 7 MET cc_start: 0.7792 (tmm) cc_final: 0.7326 (tmm) REVERT: L 13 TYR cc_start: 0.8331 (t80) cc_final: 0.8011 (t80) REVERT: A 5 LEU cc_start: 0.7768 (mt) cc_final: 0.7243 (pt) REVERT: A 24 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7407 (mmm160) REVERT: A 188 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.8077 (t-90) REVERT: A 198 MET cc_start: 0.8480 (ttm) cc_final: 0.8255 (ttm) REVERT: A 213 HIS cc_start: 0.8524 (p90) cc_final: 0.7479 (p90) REVERT: A 223 PHE cc_start: 0.8754 (t80) cc_final: 0.8446 (t80) REVERT: A 224 CYS cc_start: 0.9213 (m) cc_final: 0.7847 (t) REVERT: A 243 MET cc_start: 0.8921 (ttp) cc_final: 0.8691 (ttp) REVERT: A 247 MET cc_start: 0.9131 (mtm) cc_final: 0.8765 (mtm) REVERT: A 248 LYS cc_start: 0.9334 (mtmm) cc_final: 0.9100 (mttt) REVERT: A 256 ASN cc_start: 0.9095 (m-40) cc_final: 0.8778 (m110) REVERT: A 269 ASN cc_start: 0.9160 (m110) cc_final: 0.7672 (m-40) REVERT: A 304 GLN cc_start: 0.9400 (tt0) cc_final: 0.9107 (tm-30) REVERT: A 317 LYS cc_start: 0.8766 (pttt) cc_final: 0.8551 (pttp) REVERT: A 349 LYS cc_start: 0.9419 (mtmt) cc_final: 0.8833 (tmtt) REVERT: B 49 ARG cc_start: 0.8717 (mmt180) cc_final: 0.8328 (mmt90) REVERT: B 51 LEU cc_start: 0.9099 (mp) cc_final: 0.8778 (tp) REVERT: B 69 LEU cc_start: 0.9514 (mt) cc_final: 0.8724 (pp) REVERT: B 180 PHE cc_start: 0.8521 (m-80) cc_final: 0.6923 (m-80) REVERT: B 192 LEU cc_start: 0.8445 (mt) cc_final: 0.8117 (pt) REVERT: B 222 PHE cc_start: 0.8202 (m-80) cc_final: 0.7742 (m-80) REVERT: B 254 ASP cc_start: 0.7657 (t70) cc_final: 0.7412 (t0) REVERT: B 289 TYR cc_start: 0.7346 (m-80) cc_final: 0.6626 (m-80) REVERT: C 38 MET cc_start: 0.9202 (ptp) cc_final: 0.8985 (ptp) REVERT: D 35 HIS cc_start: 0.9004 (m-70) cc_final: 0.8766 (m-70) REVERT: D 73 ASP cc_start: 0.9018 (t70) cc_final: 0.8722 (t0) REVERT: D 78 THR cc_start: 0.8944 (m) cc_final: 0.8153 (p) REVERT: D 80 PHE cc_start: 0.8562 (m-80) cc_final: 0.8246 (m-10) REVERT: D 111 TRP cc_start: 0.8349 (m100) cc_final: 0.7827 (m-10) REVERT: D 159 ASN cc_start: 0.9247 (m110) cc_final: 0.8885 (t0) REVERT: D 165 PHE cc_start: 0.8563 (m-80) cc_final: 0.8340 (m-80) REVERT: D 227 PHE cc_start: 0.8507 (m-80) cc_final: 0.8302 (m-80) outliers start: 2 outliers final: 0 residues processed: 313 average time/residue: 0.2283 time to fit residues: 95.7630 Evaluate side-chains 247 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 181 GLN A 195 HIS B 32 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS D 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9266 Z= 0.271 Angle : 0.637 7.124 12554 Z= 0.337 Chirality : 0.043 0.153 1432 Planarity : 0.004 0.045 1579 Dihedral : 4.775 32.244 1251 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.30 % Allowed : 2.93 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.48 (0.25), residues: 1143 helix: 0.69 (0.25), residues: 404 sheet: -0.27 (0.32), residues: 258 loop : -1.15 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 36 HIS 0.006 0.002 HIS D 35 PHE 0.015 0.002 PHE B 234 TYR 0.012 0.002 TYR R 127 ARG 0.006 0.001 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 291 time to evaluate : 1.043 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: R 190 LEU cc_start: 0.9562 (mt) cc_final: 0.9357 (mt) REVERT: R 236 GLU cc_start: 0.8175 (mp0) cc_final: 0.7940 (mp0) REVERT: R 280 PHE cc_start: 0.8502 (t80) cc_final: 0.7795 (m-80) REVERT: R 293 TYR cc_start: 0.8636 (m-10) cc_final: 0.8333 (m-10) REVERT: R 295 LEU cc_start: 0.8497 (mt) cc_final: 0.8191 (mt) REVERT: R 320 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8282 (mt-10) REVERT: R 326 PHE cc_start: 0.8077 (m-10) cc_final: 0.7710 (t80) REVERT: L 7 MET cc_start: 0.7908 (tmm) cc_final: 0.7436 (tmm) REVERT: L 13 TYR cc_start: 0.8539 (t80) cc_final: 0.8308 (t80) REVERT: A 198 MET cc_start: 0.8436 (ttm) cc_final: 0.8228 (ttp) REVERT: A 213 HIS cc_start: 0.8626 (p90) cc_final: 0.7704 (p90) REVERT: A 224 CYS cc_start: 0.9227 (m) cc_final: 0.7987 (t) REVERT: A 248 LYS cc_start: 0.9370 (mtmm) cc_final: 0.9113 (mttm) REVERT: A 256 ASN cc_start: 0.9139 (m-40) cc_final: 0.8729 (m110) REVERT: A 304 GLN cc_start: 0.9412 (tt0) cc_final: 0.9120 (tm-30) REVERT: A 349 LYS cc_start: 0.9430 (mtmt) cc_final: 0.8950 (tptp) REVERT: B 49 ARG cc_start: 0.8870 (mmt180) cc_final: 0.8470 (mmt90) REVERT: B 51 LEU cc_start: 0.9133 (mp) cc_final: 0.8797 (tp) REVERT: B 57 LYS cc_start: 0.9126 (pttp) cc_final: 0.8659 (ptmt) REVERT: B 192 LEU cc_start: 0.8541 (mt) cc_final: 0.8209 (pt) REVERT: B 222 PHE cc_start: 0.8197 (m-80) cc_final: 0.7969 (m-10) REVERT: B 254 ASP cc_start: 0.7756 (t70) cc_final: 0.7539 (t0) REVERT: B 262 MET cc_start: 0.8443 (ptp) cc_final: 0.8141 (ptm) REVERT: B 283 ARG cc_start: 0.9167 (tpt170) cc_final: 0.8954 (tpt170) REVERT: B 289 TYR cc_start: 0.7732 (m-80) cc_final: 0.6350 (m-80) REVERT: C 21 MET cc_start: 0.9097 (mmm) cc_final: 0.8631 (mmm) REVERT: C 38 MET cc_start: 0.9199 (ptp) cc_final: 0.8933 (ptp) REVERT: D 45 LEU cc_start: 0.8920 (mt) cc_final: 0.8695 (mt) REVERT: D 73 ASP cc_start: 0.9058 (t70) cc_final: 0.8716 (t0) REVERT: D 78 THR cc_start: 0.8924 (m) cc_final: 0.8176 (p) REVERT: D 80 PHE cc_start: 0.8636 (m-80) cc_final: 0.8245 (m-10) REVERT: D 111 TRP cc_start: 0.8460 (m100) cc_final: 0.7922 (m-10) REVERT: D 159 ASN cc_start: 0.9333 (m110) cc_final: 0.8980 (t0) REVERT: D 164 TRP cc_start: 0.8195 (m100) cc_final: 0.7541 (m-10) REVERT: D 165 PHE cc_start: 0.8486 (m-80) cc_final: 0.8219 (m-80) REVERT: D 202 LEU cc_start: 0.9218 (tt) cc_final: 0.8659 (tt) REVERT: D 218 MET cc_start: 0.8428 (tmm) cc_final: 0.8184 (tmm) REVERT: D 227 PHE cc_start: 0.8625 (m-80) cc_final: 0.8149 (m-80) outliers start: 3 outliers final: 0 residues processed: 292 average time/residue: 0.2543 time to fit residues: 99.7558 Evaluate side-chains 225 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS ** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN B 32 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9266 Z= 0.371 Angle : 0.728 7.801 12554 Z= 0.390 Chirality : 0.045 0.173 1432 Planarity : 0.005 0.049 1579 Dihedral : 5.283 30.830 1251 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1143 helix: 0.35 (0.25), residues: 402 sheet: -0.39 (0.33), residues: 256 loop : -1.22 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP R 206 HIS 0.008 0.002 HIS D 35 PHE 0.019 0.003 PHE R 268 TYR 0.031 0.002 TYR B 124 ARG 0.007 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 1.107 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 236 GLU cc_start: 0.8552 (mp0) cc_final: 0.8226 (mp0) REVERT: R 245 MET cc_start: 0.9072 (mpp) cc_final: 0.8850 (mpp) REVERT: R 280 PHE cc_start: 0.8552 (t80) cc_final: 0.7718 (m-80) REVERT: R 293 TYR cc_start: 0.8629 (m-10) cc_final: 0.8364 (m-10) REVERT: R 320 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8156 (mt-10) REVERT: R 326 PHE cc_start: 0.8274 (m-10) cc_final: 0.7690 (t80) REVERT: R 374 MET cc_start: 0.5093 (mmt) cc_final: 0.4771 (mmt) REVERT: L 7 MET cc_start: 0.7964 (tmm) cc_final: 0.7453 (tmm) REVERT: L 13 TYR cc_start: 0.8773 (t80) cc_final: 0.8470 (t80) REVERT: A 5 LEU cc_start: 0.8204 (mm) cc_final: 0.7527 (pt) REVERT: A 188 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8174 (t-90) REVERT: A 198 MET cc_start: 0.8352 (ttm) cc_final: 0.8093 (ttp) REVERT: A 213 HIS cc_start: 0.8696 (p90) cc_final: 0.7740 (p90) REVERT: A 224 CYS cc_start: 0.9213 (m) cc_final: 0.7888 (t) REVERT: A 243 MET cc_start: 0.9123 (ttp) cc_final: 0.8364 (tmm) REVERT: A 247 MET cc_start: 0.9309 (mtm) cc_final: 0.8454 (mtp) REVERT: A 248 LYS cc_start: 0.9482 (mtmm) cc_final: 0.9276 (mttt) REVERT: A 256 ASN cc_start: 0.9148 (m-40) cc_final: 0.8748 (m110) REVERT: A 269 ASN cc_start: 0.8995 (m110) cc_final: 0.7831 (m-40) REVERT: A 304 GLN cc_start: 0.9446 (tt0) cc_final: 0.9019 (tm-30) REVERT: A 348 LEU cc_start: 0.9321 (mm) cc_final: 0.9082 (tp) REVERT: B 49 ARG cc_start: 0.8830 (mmt180) cc_final: 0.8623 (mmt180) REVERT: B 57 LYS cc_start: 0.9129 (pttp) cc_final: 0.8572 (ptpt) REVERT: B 101 MET cc_start: 0.8613 (mtm) cc_final: 0.8328 (mtm) REVERT: B 192 LEU cc_start: 0.8535 (mt) cc_final: 0.8192 (pt) REVERT: B 219 ARG cc_start: 0.8304 (tpt90) cc_final: 0.7979 (tpt90) REVERT: B 222 PHE cc_start: 0.8290 (m-80) cc_final: 0.7881 (m-80) REVERT: B 289 TYR cc_start: 0.7659 (m-80) cc_final: 0.6419 (m-80) REVERT: C 38 MET cc_start: 0.9227 (ptp) cc_final: 0.8970 (ptp) REVERT: D 34 MET cc_start: 0.8607 (tpp) cc_final: 0.8346 (tpp) REVERT: D 35 HIS cc_start: 0.9217 (m-70) cc_final: 0.8924 (m-70) REVERT: D 73 ASP cc_start: 0.9139 (t70) cc_final: 0.8398 (t0) REVERT: D 78 THR cc_start: 0.9101 (m) cc_final: 0.8417 (p) REVERT: D 80 PHE cc_start: 0.8542 (m-80) cc_final: 0.8071 (m-10) REVERT: D 111 TRP cc_start: 0.8597 (m100) cc_final: 0.8040 (m-10) REVERT: D 159 ASN cc_start: 0.9230 (m110) cc_final: 0.8987 (m110) REVERT: D 164 TRP cc_start: 0.8411 (m100) cc_final: 0.7707 (m-10) REVERT: D 165 PHE cc_start: 0.8658 (m-80) cc_final: 0.8370 (m-80) REVERT: D 202 LEU cc_start: 0.9257 (tt) cc_final: 0.8908 (tt) REVERT: D 227 PHE cc_start: 0.8525 (m-80) cc_final: 0.8198 (m-80) outliers start: 2 outliers final: 0 residues processed: 277 average time/residue: 0.2319 time to fit residues: 86.4092 Evaluate side-chains 216 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS ** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9266 Z= 0.337 Angle : 0.711 7.440 12554 Z= 0.379 Chirality : 0.045 0.197 1432 Planarity : 0.005 0.057 1579 Dihedral : 5.296 30.696 1251 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.95 (0.24), residues: 1143 helix: 0.12 (0.25), residues: 407 sheet: -0.48 (0.34), residues: 247 loop : -1.26 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP R 206 HIS 0.010 0.002 HIS B 142 PHE 0.023 0.002 PHE A 307 TYR 0.025 0.002 TYR R 369 ARG 0.004 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 0.987 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: R 190 LEU cc_start: 0.9579 (mt) cc_final: 0.9375 (mt) REVERT: R 236 GLU cc_start: 0.8543 (mp0) cc_final: 0.8255 (mp0) REVERT: R 245 MET cc_start: 0.9125 (mpp) cc_final: 0.8920 (mpp) REVERT: R 280 PHE cc_start: 0.8539 (t80) cc_final: 0.7620 (m-80) REVERT: R 300 MET cc_start: 0.7341 (tmm) cc_final: 0.7005 (tmm) REVERT: R 320 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8200 (mt-10) REVERT: R 326 PHE cc_start: 0.8336 (m-10) cc_final: 0.7706 (t80) REVERT: R 374 MET cc_start: 0.4995 (mmt) cc_final: 0.4710 (mmt) REVERT: L 7 MET cc_start: 0.7969 (tmm) cc_final: 0.7414 (tmm) REVERT: A 213 HIS cc_start: 0.8699 (p90) cc_final: 0.7790 (p90) REVERT: A 224 CYS cc_start: 0.9141 (m) cc_final: 0.8151 (t) REVERT: A 243 MET cc_start: 0.9121 (ttp) cc_final: 0.8390 (tmm) REVERT: A 247 MET cc_start: 0.9273 (mtm) cc_final: 0.8506 (mtp) REVERT: A 256 ASN cc_start: 0.9152 (m-40) cc_final: 0.8610 (m110) REVERT: A 275 GLU cc_start: 0.9313 (tm-30) cc_final: 0.8948 (tm-30) REVERT: A 304 GLN cc_start: 0.9507 (tt0) cc_final: 0.9096 (tm-30) REVERT: A 348 LEU cc_start: 0.9302 (mm) cc_final: 0.8983 (tp) REVERT: A 349 LYS cc_start: 0.9414 (mtmt) cc_final: 0.9208 (mtpt) REVERT: B 49 ARG cc_start: 0.8829 (mmt180) cc_final: 0.8491 (mmt90) REVERT: B 51 LEU cc_start: 0.9168 (mp) cc_final: 0.8838 (tp) REVERT: B 57 LYS cc_start: 0.9124 (pttp) cc_final: 0.8507 (ptpt) REVERT: B 101 MET cc_start: 0.8598 (mtm) cc_final: 0.8298 (mtm) REVERT: B 124 TYR cc_start: 0.8074 (m-10) cc_final: 0.7854 (m-10) REVERT: B 192 LEU cc_start: 0.8654 (mt) cc_final: 0.8219 (pt) REVERT: B 199 PHE cc_start: 0.9001 (p90) cc_final: 0.8731 (p90) REVERT: B 222 PHE cc_start: 0.8274 (m-80) cc_final: 0.7585 (m-80) REVERT: B 289 TYR cc_start: 0.7559 (m-80) cc_final: 0.6380 (m-80) REVERT: C 38 MET cc_start: 0.9214 (ptp) cc_final: 0.8954 (ptp) REVERT: D 29 PHE cc_start: 0.9143 (t80) cc_final: 0.8865 (t80) REVERT: D 35 HIS cc_start: 0.9148 (m-70) cc_final: 0.8703 (m-70) REVERT: D 73 ASP cc_start: 0.9162 (t70) cc_final: 0.8384 (t0) REVERT: D 78 THR cc_start: 0.8884 (m) cc_final: 0.8645 (p) REVERT: D 80 PHE cc_start: 0.8518 (m-80) cc_final: 0.8284 (m-80) REVERT: D 108 PHE cc_start: 0.9189 (m-80) cc_final: 0.8828 (m-80) REVERT: D 111 TRP cc_start: 0.8513 (m100) cc_final: 0.8075 (m-10) REVERT: D 159 ASN cc_start: 0.9201 (m110) cc_final: 0.8680 (t0) REVERT: D 164 TRP cc_start: 0.8360 (m100) cc_final: 0.7891 (m-10) REVERT: D 202 LEU cc_start: 0.9234 (tt) cc_final: 0.8817 (tt) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2332 time to fit residues: 84.5621 Evaluate side-chains 221 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 105 optimal weight: 9.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS A 188 HIS A 294 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9266 Z= 0.187 Angle : 0.663 7.329 12554 Z= 0.345 Chirality : 0.045 0.160 1432 Planarity : 0.004 0.055 1579 Dihedral : 4.938 26.560 1251 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.30 % Allowed : 1.01 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.69 (0.25), residues: 1143 helix: 0.44 (0.25), residues: 410 sheet: -0.43 (0.33), residues: 256 loop : -1.18 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 206 HIS 0.006 0.001 HIS A 213 PHE 0.023 0.002 PHE B 278 TYR 0.023 0.002 TYR R 369 ARG 0.004 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 297 time to evaluate : 1.018 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: R 94 ILE cc_start: 0.7294 (mt) cc_final: 0.7040 (mm) REVERT: R 253 ARG cc_start: 0.7438 (mtt180) cc_final: 0.6971 (mtp180) REVERT: R 280 PHE cc_start: 0.8431 (t80) cc_final: 0.7626 (m-80) REVERT: R 282 PHE cc_start: 0.8769 (t80) cc_final: 0.8545 (t80) REVERT: R 293 TYR cc_start: 0.8570 (m-10) cc_final: 0.8308 (m-80) REVERT: R 299 GLU cc_start: 0.5899 (mp0) cc_final: 0.5661 (mp0) REVERT: R 320 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8202 (mt-10) REVERT: R 326 PHE cc_start: 0.8241 (m-10) cc_final: 0.7594 (t80) REVERT: R 374 MET cc_start: 0.4222 (mmt) cc_final: 0.3878 (mmt) REVERT: R 381 ILE cc_start: 0.8796 (tp) cc_final: 0.8578 (tp) REVERT: L 7 MET cc_start: 0.7726 (tmm) cc_final: 0.7127 (tmm) REVERT: L 13 TYR cc_start: 0.8752 (t80) cc_final: 0.8549 (t80) REVERT: A 188 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.8148 (t-90) REVERT: A 200 ASP cc_start: 0.8597 (t0) cc_final: 0.8210 (t0) REVERT: A 213 HIS cc_start: 0.8748 (p90) cc_final: 0.7947 (p90) REVERT: A 224 CYS cc_start: 0.9126 (m) cc_final: 0.8064 (t) REVERT: A 243 MET cc_start: 0.9075 (ttp) cc_final: 0.8325 (tmm) REVERT: A 247 MET cc_start: 0.9356 (mtm) cc_final: 0.8530 (mtm) REVERT: A 256 ASN cc_start: 0.9174 (m-40) cc_final: 0.8713 (m110) REVERT: A 274 PHE cc_start: 0.9207 (t80) cc_final: 0.8877 (t80) REVERT: A 296 TYR cc_start: 0.8483 (t80) cc_final: 0.7867 (t80) REVERT: A 304 GLN cc_start: 0.9438 (tt0) cc_final: 0.8510 (tm-30) REVERT: A 348 LEU cc_start: 0.9274 (mm) cc_final: 0.8992 (tp) REVERT: B 49 ARG cc_start: 0.8839 (mmt180) cc_final: 0.8571 (mmt90) REVERT: B 57 LYS cc_start: 0.9137 (pttp) cc_final: 0.8603 (ptpt) REVERT: B 61 MET cc_start: 0.8951 (tmm) cc_final: 0.8729 (tmm) REVERT: B 124 TYR cc_start: 0.7827 (m-10) cc_final: 0.7613 (m-10) REVERT: B 138 GLU cc_start: 0.8448 (pm20) cc_final: 0.8208 (pt0) REVERT: B 192 LEU cc_start: 0.8529 (mt) cc_final: 0.8204 (pt) REVERT: B 198 LEU cc_start: 0.9267 (mt) cc_final: 0.9050 (mt) REVERT: B 219 ARG cc_start: 0.8247 (tpt90) cc_final: 0.8001 (tpt90) REVERT: B 283 ARG cc_start: 0.9138 (tpt170) cc_final: 0.8847 (tpt170) REVERT: B 289 TYR cc_start: 0.7415 (m-80) cc_final: 0.6352 (m-80) REVERT: B 292 PHE cc_start: 0.9207 (m-10) cc_final: 0.8628 (m-80) REVERT: D 29 PHE cc_start: 0.8856 (t80) cc_final: 0.8541 (t80) REVERT: D 35 HIS cc_start: 0.8776 (m90) cc_final: 0.8521 (m-70) REVERT: D 73 ASP cc_start: 0.9016 (t70) cc_final: 0.8287 (t0) REVERT: D 111 TRP cc_start: 0.8194 (m100) cc_final: 0.7772 (m-10) REVERT: D 159 ASN cc_start: 0.9318 (m110) cc_final: 0.8872 (t0) REVERT: D 164 TRP cc_start: 0.8141 (m100) cc_final: 0.7411 (m-10) REVERT: D 165 PHE cc_start: 0.8601 (m-80) cc_final: 0.8175 (m-80) REVERT: D 202 LEU cc_start: 0.9193 (tt) cc_final: 0.8738 (tt) REVERT: D 218 MET cc_start: 0.8392 (tmm) cc_final: 0.7956 (tmm) REVERT: D 227 PHE cc_start: 0.8555 (m-80) cc_final: 0.8179 (m-80) outliers start: 3 outliers final: 2 residues processed: 298 average time/residue: 0.2308 time to fit residues: 92.3527 Evaluate side-chains 236 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 GLN A 188 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9266 Z= 0.215 Angle : 0.664 8.296 12554 Z= 0.346 Chirality : 0.045 0.192 1432 Planarity : 0.005 0.082 1579 Dihedral : 4.861 25.004 1251 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.64 (0.25), residues: 1143 helix: 0.47 (0.25), residues: 408 sheet: -0.42 (0.33), residues: 261 loop : -1.14 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 336 HIS 0.008 0.002 HIS B 142 PHE 0.023 0.002 PHE A 307 TYR 0.025 0.002 TYR R 369 ARG 0.005 0.001 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 1.021 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: R 236 GLU cc_start: 0.8567 (mp0) cc_final: 0.8337 (mp0) REVERT: R 253 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6810 (mtp180) REVERT: R 280 PHE cc_start: 0.8468 (t80) cc_final: 0.7642 (m-80) REVERT: R 293 TYR cc_start: 0.8556 (m-10) cc_final: 0.8273 (m-80) REVERT: R 320 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8193 (mt-10) REVERT: R 326 PHE cc_start: 0.8234 (m-10) cc_final: 0.7533 (t80) REVERT: R 374 MET cc_start: 0.4389 (mmt) cc_final: 0.4049 (mmt) REVERT: L 7 MET cc_start: 0.7744 (tmm) cc_final: 0.7330 (tmm) REVERT: L 13 TYR cc_start: 0.8808 (t80) cc_final: 0.8578 (t80) REVERT: A 200 ASP cc_start: 0.8583 (t0) cc_final: 0.8212 (t0) REVERT: A 213 HIS cc_start: 0.8758 (p90) cc_final: 0.7941 (p90) REVERT: A 224 CYS cc_start: 0.9215 (m) cc_final: 0.8212 (p) REVERT: A 243 MET cc_start: 0.9107 (ttp) cc_final: 0.8307 (tmm) REVERT: A 247 MET cc_start: 0.9368 (mtm) cc_final: 0.8252 (mtm) REVERT: A 274 PHE cc_start: 0.9237 (t80) cc_final: 0.8892 (t80) REVERT: A 275 GLU cc_start: 0.9266 (tm-30) cc_final: 0.9038 (tm-30) REVERT: A 304 GLN cc_start: 0.9444 (tt0) cc_final: 0.8674 (tm-30) REVERT: A 348 LEU cc_start: 0.9254 (mm) cc_final: 0.8814 (tp) REVERT: A 349 LYS cc_start: 0.9422 (mtmt) cc_final: 0.9221 (mtmt) REVERT: B 57 LYS cc_start: 0.9162 (pttp) cc_final: 0.8621 (ptpt) REVERT: B 69 LEU cc_start: 0.9569 (mt) cc_final: 0.8805 (pp) REVERT: B 101 MET cc_start: 0.8725 (mtm) cc_final: 0.8456 (mpp) REVERT: B 124 TYR cc_start: 0.7834 (m-10) cc_final: 0.7612 (m-10) REVERT: B 192 LEU cc_start: 0.8564 (mt) cc_final: 0.8184 (pt) REVERT: B 219 ARG cc_start: 0.8281 (tpt90) cc_final: 0.8034 (tpt90) REVERT: B 283 ARG cc_start: 0.9166 (tpt170) cc_final: 0.8890 (tpt170) REVERT: B 289 TYR cc_start: 0.7343 (m-80) cc_final: 0.6344 (m-80) REVERT: D 43 LYS cc_start: 0.8990 (pttp) cc_final: 0.8604 (pptt) REVERT: D 73 ASP cc_start: 0.8856 (t70) cc_final: 0.8535 (t0) REVERT: D 111 TRP cc_start: 0.8386 (m100) cc_final: 0.7939 (m-10) REVERT: D 159 ASN cc_start: 0.9290 (m110) cc_final: 0.8845 (t0) REVERT: D 164 TRP cc_start: 0.8087 (m100) cc_final: 0.7566 (m-10) REVERT: D 165 PHE cc_start: 0.8482 (m-80) cc_final: 0.8275 (m-80) REVERT: D 202 LEU cc_start: 0.9140 (tt) cc_final: 0.8631 (tt) REVERT: D 218 MET cc_start: 0.8417 (tmm) cc_final: 0.8179 (tmm) REVERT: D 225 LEU cc_start: 0.7639 (mt) cc_final: 0.7350 (mt) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.2248 time to fit residues: 84.2995 Evaluate side-chains 219 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS R 181 GLN A 188 HIS A 294 ASN A 304 GLN B 32 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9266 Z= 0.261 Angle : 0.692 8.087 12554 Z= 0.362 Chirality : 0.045 0.185 1432 Planarity : 0.005 0.094 1579 Dihedral : 5.017 25.932 1251 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.20 % Allowed : 0.71 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.68 (0.25), residues: 1143 helix: 0.46 (0.25), residues: 408 sheet: -0.39 (0.33), residues: 258 loop : -1.20 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 336 HIS 0.008 0.002 HIS A 213 PHE 0.029 0.002 PHE D 227 TYR 0.025 0.002 TYR R 369 ARG 0.007 0.001 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 1.023 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 236 GLU cc_start: 0.8617 (mp0) cc_final: 0.8339 (mp0) REVERT: R 245 MET cc_start: 0.8983 (mpp) cc_final: 0.8677 (mpp) REVERT: R 253 ARG cc_start: 0.7430 (mtt180) cc_final: 0.7037 (mtp180) REVERT: R 280 PHE cc_start: 0.8481 (t80) cc_final: 0.7678 (m-80) REVERT: R 293 TYR cc_start: 0.8569 (m-10) cc_final: 0.8276 (m-80) REVERT: R 320 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8196 (mt-10) REVERT: R 326 PHE cc_start: 0.8282 (m-10) cc_final: 0.7548 (t80) REVERT: R 374 MET cc_start: 0.4353 (mmt) cc_final: 0.4008 (mmt) REVERT: L 7 MET cc_start: 0.7735 (tmm) cc_final: 0.7326 (tmm) REVERT: A 9 ASP cc_start: 0.9156 (m-30) cc_final: 0.8949 (m-30) REVERT: A 188 HIS cc_start: 0.8491 (OUTLIER) cc_final: 0.8225 (t-90) REVERT: A 198 MET cc_start: 0.8527 (ttm) cc_final: 0.8274 (ttp) REVERT: A 200 ASP cc_start: 0.8544 (t0) cc_final: 0.8178 (t0) REVERT: A 213 HIS cc_start: 0.8801 (p90) cc_final: 0.8029 (p90) REVERT: A 224 CYS cc_start: 0.9224 (m) cc_final: 0.8242 (p) REVERT: A 243 MET cc_start: 0.9038 (ttp) cc_final: 0.8468 (tmm) REVERT: A 247 MET cc_start: 0.9397 (mtm) cc_final: 0.8587 (mtm) REVERT: A 274 PHE cc_start: 0.9257 (t80) cc_final: 0.8886 (t80) REVERT: A 304 GLN cc_start: 0.9515 (tt0) cc_final: 0.8608 (tm-30) REVERT: A 348 LEU cc_start: 0.9250 (mm) cc_final: 0.8875 (tp) REVERT: B 57 LYS cc_start: 0.9182 (pttp) cc_final: 0.8613 (ptpt) REVERT: B 61 MET cc_start: 0.8784 (tmm) cc_final: 0.8566 (tmm) REVERT: B 192 LEU cc_start: 0.8555 (mt) cc_final: 0.8183 (pt) REVERT: B 219 ARG cc_start: 0.8284 (tpt90) cc_final: 0.8043 (tpt90) REVERT: B 262 MET cc_start: 0.7886 (ptp) cc_final: 0.7642 (ptp) REVERT: B 289 TYR cc_start: 0.7384 (m-80) cc_final: 0.6470 (m-80) REVERT: D 43 LYS cc_start: 0.9002 (pttp) cc_final: 0.8574 (pptt) REVERT: D 73 ASP cc_start: 0.8863 (t70) cc_final: 0.8451 (t0) REVERT: D 80 PHE cc_start: 0.8398 (m-80) cc_final: 0.8190 (m-10) REVERT: D 111 TRP cc_start: 0.8451 (m100) cc_final: 0.7978 (m-10) REVERT: D 159 ASN cc_start: 0.9158 (m110) cc_final: 0.8626 (t0) REVERT: D 164 TRP cc_start: 0.8143 (m100) cc_final: 0.7861 (m-10) REVERT: D 202 LEU cc_start: 0.9172 (tt) cc_final: 0.8692 (tt) outliers start: 2 outliers final: 1 residues processed: 264 average time/residue: 0.2318 time to fit residues: 82.0633 Evaluate side-chains 216 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 0.0370 chunk 37 optimal weight: 0.0470 chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 HIS ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060915 restraints weight = 41094.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063065 restraints weight = 27376.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.064656 restraints weight = 20074.024| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9266 Z= 0.183 Angle : 0.686 7.872 12554 Z= 0.353 Chirality : 0.045 0.185 1432 Planarity : 0.005 0.077 1579 Dihedral : 4.811 25.695 1251 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.57 (0.25), residues: 1143 helix: 0.44 (0.24), residues: 409 sheet: -0.28 (0.34), residues: 253 loop : -1.06 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP R 336 HIS 0.018 0.002 HIS R 340 PHE 0.025 0.002 PHE D 227 TYR 0.025 0.002 TYR R 369 ARG 0.026 0.001 ARG R 343 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.03 seconds wall clock time: 45 minutes 24.35 seconds (2724.35 seconds total)