Starting phenix.real_space_refine on Sat Aug 3 17:43:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/08_2024/8xog_38528_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/08_2024/8xog_38528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/08_2024/8xog_38528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/08_2024/8xog_38528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/08_2024/8xog_38528_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/08_2024/8xog_38528_neut.cif" } resolution = 2.9 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= 0.032 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 53 5.16 5 C 5535 2.51 5 N 1509 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R GLU 89": "OE1" <-> "OE2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R GLU 218": "OE1" <-> "OE2" Residue "R GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1852 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2552 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1724 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 423 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2155 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.33, per 1000 atoms: 0.61 Number of scatterers: 8708 At special positions: 0 Unit cell: (94.76, 120.304, 124.424, 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 53 16.00 O 1611 8.00 N 1509 7.00 C 5535 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.70 Conformation dependent library (CDL) restraints added in 1.5 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 40.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 16 through 40 removed outlier: 3.776A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.604A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.954A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.488A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.535A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.644A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 25 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.025A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 53 through 87 removed outlier: 4.624A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 88 through 91 Processing helix chain 'R' and resid 92 through 116 removed outlier: 3.510A pdb=" N LEU R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU R 115 " --> pdb=" O ASP R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 125 removed outlier: 4.186A pdb=" N ASP R 125 " --> pdb=" O GLU R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 161 Processing helix chain 'R' and resid 170 through 200 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 211 through 223 Processing helix chain 'R' and resid 223 through 246 Processing helix chain 'R' and resid 254 through 285 removed outlier: 3.600A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.623A pdb=" N ASN R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 342 removed outlier: 3.624A pdb=" N ARG R 332 " --> pdb=" O GLY R 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.939A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.029A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.532A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.651A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.724A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.892A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.501A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.440A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.695A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.548A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.840A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.746A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1293 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: 2.90 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2795 1.34 - 1.45: 1219 1.45 - 1.57: 4792 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8882 Sorted by residual: bond pdb=" N SER B 74 " pdb=" CA SER B 74 " ideal model delta sigma weight residual 1.455 1.421 0.033 1.29e-02 6.01e+03 6.62e+00 bond pdb=" C TYR B 289 " pdb=" N ASP B 290 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.52e-02 4.33e+03 4.68e+00 bond pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.32e-02 5.74e+03 4.64e+00 bond pdb=" CA SER B 74 " pdb=" CB SER B 74 " ideal model delta sigma weight residual 1.535 1.497 0.039 1.90e-02 2.77e+03 4.12e+00 bond pdb=" CA SER B 74 " pdb=" C SER B 74 " ideal model delta sigma weight residual 1.522 1.497 0.025 1.24e-02 6.50e+03 4.06e+00 ... (remaining 8877 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.28: 168 106.28 - 113.24: 4885 113.24 - 120.19: 3123 120.19 - 127.14: 3761 127.14 - 134.10: 96 Bond angle restraints: 12033 Sorted by residual: angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" C ASP B 290 " ideal model delta sigma weight residual 113.20 107.58 5.62 1.21e+00 6.83e-01 2.16e+01 angle pdb=" CA PRO R 192 " pdb=" N PRO R 192 " pdb=" CD PRO R 192 " ideal model delta sigma weight residual 112.00 106.53 5.47 1.40e+00 5.10e-01 1.53e+01 angle pdb=" C SER R 325 " pdb=" N PHE R 326 " pdb=" CA PHE R 326 " ideal model delta sigma weight residual 122.86 117.29 5.57 1.53e+00 4.27e-01 1.32e+01 angle pdb=" CA SER B 74 " pdb=" CB SER B 74 " pdb=" OG SER B 74 " ideal model delta sigma weight residual 111.10 105.40 5.70 2.00e+00 2.50e-01 8.13e+00 angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " ideal model delta sigma weight residual 110.42 114.92 -4.50 1.62e+00 3.81e-01 7.71e+00 ... (remaining 12028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4709 17.85 - 35.71: 430 35.71 - 53.56: 96 53.56 - 71.42: 19 71.42 - 89.27: 9 Dihedral angle restraints: 5263 sinusoidal: 2030 harmonic: 3233 Sorted by residual: dihedral pdb=" CA PHE R 326 " pdb=" C PHE R 326 " pdb=" N LEU R 327 " pdb=" CA LEU R 327 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE R 223 " pdb=" C PHE R 223 " pdb=" N ILE R 224 " pdb=" CA ILE R 224 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ILE A 207 " pdb=" C ILE A 207 " pdb=" N PHE A 208 " pdb=" CA PHE A 208 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 5260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1050 0.042 - 0.083: 227 0.083 - 0.125: 82 0.125 - 0.166: 14 0.166 - 0.208: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA ASP B 290 " pdb=" N ASP B 290 " pdb=" C ASP B 290 " pdb=" CB ASP B 290 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TYR A 391 " pdb=" N TYR A 391 " pdb=" C TYR A 391 " pdb=" CB TYR A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1371 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 191 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO R 192 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO R 192 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO R 192 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 219 " -0.156 9.50e-02 1.11e+02 7.03e-02 3.28e+00 pdb=" NE ARG B 219 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 219 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 219 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 219 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 73 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C ALA B 73 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA B 73 " 0.012 2.00e-02 2.50e+03 pdb=" N SER B 74 " 0.010 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2092 2.79 - 3.32: 8526 3.32 - 3.84: 14308 3.84 - 4.37: 17360 4.37 - 4.90: 29977 Nonbonded interactions: 72263 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.263 3.040 nonbonded pdb=" OG SER E 17 " pdb=" O THR E 84 " model vdw 2.264 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OD1 ASP A 240 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.285 3.040 nonbonded pdb=" O ASN A 392 " pdb=" ND2 ASN A 392 " model vdw 2.325 3.120 ... (remaining 72258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.590 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: 0.060 Set scattering table: 0.090 Process input model: 27.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 0.060 8882 Z= 0.218 Angle : 0.561 8.446 12033 Z= 0.318 Chirality : 0.041 0.208 1374 Planarity : 0.005 0.115 1529 Dihedral : 14.841 89.272 3167 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.21 % Allowed : 14.41 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1091 helix: 1.40 (0.26), residues: 401 sheet: -0.07 (0.31), residues: 274 loop : 0.24 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS B 91 PHE 0.023 0.001 PHE R 326 TYR 0.009 0.001 TYR A 391 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7248 (tt0) cc_final: 0.6554 (mt0) REVERT: A 232 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7684 (ttp-170) REVERT: A 391 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.6070 (m-80) REVERT: G 58 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6937 (mt-10) REVERT: R 141 MET cc_start: 0.6606 (ptp) cc_final: 0.5929 (tmt) outliers start: 2 outliers final: 0 residues processed: 118 average time/residue: 1.0760 time to fit residues: 136.6032 Evaluate side-chains 108 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 175 GLN B 259 GLN E 194 ASN E 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8882 Z= 0.330 Angle : 0.642 10.547 12033 Z= 0.339 Chirality : 0.046 0.174 1374 Planarity : 0.005 0.072 1529 Dihedral : 5.064 57.644 1205 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.31 % Allowed : 14.94 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1091 helix: 1.29 (0.25), residues: 401 sheet: 0.25 (0.32), residues: 267 loop : 0.35 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.007 0.001 HIS B 91 PHE 0.019 0.002 PHE R 227 TYR 0.013 0.001 TYR A 339 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7105 (mt-10) REVERT: A 213 GLN cc_start: 0.7361 (tt0) cc_final: 0.6608 (mt0) REVERT: A 391 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: G 58 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6993 (mt-10) REVERT: R 141 MET cc_start: 0.6870 (ptp) cc_final: 0.6039 (tmt) outliers start: 31 outliers final: 12 residues processed: 128 average time/residue: 0.9717 time to fit residues: 134.8237 Evaluate side-chains 109 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8882 Z= 0.248 Angle : 0.580 10.453 12033 Z= 0.305 Chirality : 0.043 0.163 1374 Planarity : 0.004 0.055 1529 Dihedral : 4.880 58.129 1205 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.31 % Allowed : 15.26 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1091 helix: 1.39 (0.25), residues: 403 sheet: 0.22 (0.32), residues: 265 loop : 0.37 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR A 339 ARG 0.003 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6978 (mt-10) REVERT: A 213 GLN cc_start: 0.7407 (tt0) cc_final: 0.6662 (mt0) REVERT: A 391 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.5862 (m-80) REVERT: E 230 MET cc_start: 0.2420 (ttp) cc_final: 0.1991 (mpt) REVERT: G 58 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6913 (mt-10) REVERT: R 141 MET cc_start: 0.6854 (ptp) cc_final: 0.6013 (tmt) outliers start: 31 outliers final: 14 residues processed: 125 average time/residue: 0.9668 time to fit residues: 131.0833 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 247 HIS Chi-restraints excluded: chain R residue 311 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN B 175 GLN R 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8882 Z= 0.197 Angle : 0.554 13.039 12033 Z= 0.288 Chirality : 0.042 0.164 1374 Planarity : 0.004 0.047 1529 Dihedral : 4.713 58.471 1205 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.09 % Allowed : 16.33 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1091 helix: 1.61 (0.25), residues: 403 sheet: 0.11 (0.32), residues: 269 loop : 0.42 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR B 289 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 213 GLN cc_start: 0.7426 (tt0) cc_final: 0.6677 (mt0) REVERT: A 299 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: A 391 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.5930 (m-80) REVERT: B 165 THR cc_start: 0.7771 (p) cc_final: 0.7551 (t) REVERT: B 178 THR cc_start: 0.7653 (OUTLIER) cc_final: 0.7450 (p) REVERT: B 251 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7941 (mmt180) REVERT: E 230 MET cc_start: 0.2459 (ttp) cc_final: 0.2007 (mpt) REVERT: G 58 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6870 (mt-10) REVERT: R 141 MET cc_start: 0.6813 (ptp) cc_final: 0.5997 (tmt) outliers start: 29 outliers final: 14 residues processed: 118 average time/residue: 1.0023 time to fit residues: 127.9253 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0010 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8882 Z= 0.184 Angle : 0.536 13.746 12033 Z= 0.280 Chirality : 0.042 0.160 1374 Planarity : 0.004 0.042 1529 Dihedral : 4.622 58.544 1205 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.88 % Allowed : 17.50 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1091 helix: 1.74 (0.26), residues: 403 sheet: 0.14 (0.32), residues: 269 loop : 0.36 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 326 TYR 0.011 0.001 TYR B 289 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6704 (mt0) REVERT: A 232 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7538 (ttp-170) REVERT: A 299 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7437 (pm20) REVERT: A 391 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.5863 (m-80) REVERT: B 153 ASP cc_start: 0.6626 (m-30) cc_final: 0.6274 (t70) REVERT: B 178 THR cc_start: 0.7640 (OUTLIER) cc_final: 0.7437 (p) REVERT: B 251 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7681 (mmt-90) REVERT: B 260 GLU cc_start: 0.8012 (tt0) cc_final: 0.7697 (tt0) REVERT: E 188 LEU cc_start: 0.3932 (mt) cc_final: 0.3542 (pt) REVERT: E 230 MET cc_start: 0.2426 (ttp) cc_final: 0.1912 (mpt) REVERT: G 58 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6854 (mt-10) REVERT: R 141 MET cc_start: 0.6835 (ptp) cc_final: 0.6011 (tmt) outliers start: 27 outliers final: 13 residues processed: 125 average time/residue: 1.0266 time to fit residues: 138.6444 Evaluate side-chains 119 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8882 Z= 0.158 Angle : 0.549 15.109 12033 Z= 0.278 Chirality : 0.041 0.155 1374 Planarity : 0.004 0.038 1529 Dihedral : 4.480 58.784 1205 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 18.89 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1091 helix: 1.85 (0.26), residues: 403 sheet: 0.29 (0.32), residues: 260 loop : 0.17 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 326 TYR 0.011 0.001 TYR B 289 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7004 (mt-10) REVERT: A 213 GLN cc_start: 0.7434 (tt0) cc_final: 0.6691 (mt0) REVERT: A 232 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7582 (ttp-170) REVERT: A 299 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: A 370 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: A 391 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.5832 (m-80) REVERT: B 153 ASP cc_start: 0.6587 (m-30) cc_final: 0.6314 (t70) REVERT: B 178 THR cc_start: 0.7585 (OUTLIER) cc_final: 0.7343 (p) REVERT: B 251 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7685 (mmt-90) REVERT: B 260 GLU cc_start: 0.8005 (tt0) cc_final: 0.7644 (tt0) REVERT: E 34 MET cc_start: 0.4418 (mmm) cc_final: 0.3767 (mmm) REVERT: E 188 LEU cc_start: 0.3946 (mt) cc_final: 0.3532 (pt) REVERT: E 230 MET cc_start: 0.2371 (ttp) cc_final: 0.1932 (mpt) REVERT: G 58 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6818 (mt-10) REVERT: R 141 MET cc_start: 0.6816 (ptp) cc_final: 0.6018 (tmt) REVERT: R 334 LYS cc_start: 0.6707 (tttp) cc_final: 0.6407 (tttp) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 1.1022 time to fit residues: 145.8461 Evaluate side-chains 122 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 87 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN A 392 ASN B 175 GLN ** R 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8882 Z= 0.276 Angle : 0.599 15.610 12033 Z= 0.305 Chirality : 0.043 0.177 1374 Planarity : 0.004 0.039 1529 Dihedral : 4.743 59.144 1205 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.99 % Allowed : 19.64 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1091 helix: 1.74 (0.26), residues: 397 sheet: 0.19 (0.32), residues: 275 loop : 0.26 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE R 326 TYR 0.013 0.001 TYR A 339 ARG 0.008 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6904 (mt-10) REVERT: A 213 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6703 (mt0) REVERT: A 232 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7487 (ttp-170) REVERT: A 266 LEU cc_start: 0.8204 (mt) cc_final: 0.7952 (mm) REVERT: A 299 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: A 370 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: A 391 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.5889 (m-80) REVERT: B 153 ASP cc_start: 0.6717 (m-30) cc_final: 0.6345 (t70) REVERT: B 178 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7418 (p) REVERT: B 251 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7580 (mmt-90) REVERT: B 260 GLU cc_start: 0.8036 (tt0) cc_final: 0.7484 (tt0) REVERT: E 34 MET cc_start: 0.4553 (mmm) cc_final: 0.4216 (mmm) REVERT: R 141 MET cc_start: 0.6901 (ptp) cc_final: 0.6031 (tmt) REVERT: R 334 LYS cc_start: 0.6725 (tttp) cc_final: 0.6519 (tttp) outliers start: 28 outliers final: 13 residues processed: 116 average time/residue: 1.0712 time to fit residues: 133.9519 Evaluate side-chains 112 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 91 MET Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.0000 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 392 ASN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8882 Z= 0.160 Angle : 0.546 16.273 12033 Z= 0.278 Chirality : 0.041 0.143 1374 Planarity : 0.004 0.038 1529 Dihedral : 4.486 59.097 1205 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.45 % Allowed : 20.38 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1091 helix: 1.95 (0.26), residues: 397 sheet: 0.22 (0.32), residues: 267 loop : 0.17 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR B 289 ARG 0.010 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 213 GLN cc_start: 0.7449 (tt0) cc_final: 0.6695 (mt0) REVERT: A 232 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7526 (ttp-170) REVERT: A 299 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: A 391 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.5887 (m-80) REVERT: B 153 ASP cc_start: 0.6673 (m-30) cc_final: 0.6362 (t70) REVERT: B 178 THR cc_start: 0.7551 (OUTLIER) cc_final: 0.7313 (p) REVERT: B 251 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7626 (mmt-90) REVERT: B 260 GLU cc_start: 0.8022 (tt0) cc_final: 0.7628 (tt0) REVERT: E 34 MET cc_start: 0.4569 (mmm) cc_final: 0.3966 (mmm) REVERT: E 230 MET cc_start: 0.2467 (ttp) cc_final: 0.1932 (mpt) REVERT: R 141 MET cc_start: 0.6803 (ptp) cc_final: 0.5980 (tmt) outliers start: 23 outliers final: 15 residues processed: 117 average time/residue: 1.1206 time to fit residues: 140.8150 Evaluate side-chains 116 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 165 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN A 392 ASN B 175 GLN B 266 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8882 Z= 0.165 Angle : 0.562 16.096 12033 Z= 0.285 Chirality : 0.041 0.145 1374 Planarity : 0.004 0.042 1529 Dihedral : 4.387 55.011 1205 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.03 % Allowed : 21.13 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1091 helix: 1.95 (0.26), residues: 397 sheet: 0.24 (0.32), residues: 264 loop : 0.12 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE R 326 TYR 0.011 0.001 TYR B 289 ARG 0.010 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 213 GLN cc_start: 0.7456 (tt0) cc_final: 0.6753 (mt0) REVERT: A 232 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7629 (ttp-170) REVERT: A 299 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: A 391 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.5686 (m-80) REVERT: B 153 ASP cc_start: 0.6656 (m-30) cc_final: 0.6400 (t70) REVERT: B 178 THR cc_start: 0.7540 (OUTLIER) cc_final: 0.7292 (p) REVERT: B 251 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7643 (mmt-90) REVERT: B 260 GLU cc_start: 0.8002 (tt0) cc_final: 0.7604 (tt0) REVERT: E 34 MET cc_start: 0.4513 (mmm) cc_final: 0.3834 (mmm) REVERT: E 230 MET cc_start: 0.2476 (ttp) cc_final: 0.1986 (mpt) REVERT: R 141 MET cc_start: 0.6797 (ptp) cc_final: 0.5993 (tmt) REVERT: R 218 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7290 (tp30) outliers start: 19 outliers final: 11 residues processed: 116 average time/residue: 1.1042 time to fit residues: 137.8156 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 247 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 294 GLN A 392 ASN B 175 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8882 Z= 0.186 Angle : 0.567 15.880 12033 Z= 0.285 Chirality : 0.042 0.157 1374 Planarity : 0.004 0.040 1529 Dihedral : 4.460 58.259 1205 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.92 % Allowed : 21.13 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1091 helix: 1.91 (0.26), residues: 396 sheet: 0.22 (0.32), residues: 269 loop : 0.16 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 326 TYR 0.010 0.001 TYR B 289 ARG 0.010 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6966 (mt-10) REVERT: A 213 GLN cc_start: 0.7440 (tt0) cc_final: 0.6704 (mt0) REVERT: A 232 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7650 (ttp-170) REVERT: A 299 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: A 391 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.5763 (m-80) REVERT: B 153 ASP cc_start: 0.6668 (m-30) cc_final: 0.6403 (t70) REVERT: B 175 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7376 (pt0) REVERT: B 178 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7291 (p) REVERT: B 251 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7594 (mmt-90) REVERT: B 260 GLU cc_start: 0.7989 (tt0) cc_final: 0.7463 (tt0) REVERT: E 34 MET cc_start: 0.4588 (mmm) cc_final: 0.4005 (mmm) REVERT: E 140 MET cc_start: 0.1400 (ptp) cc_final: 0.0850 (ptm) REVERT: E 230 MET cc_start: 0.2496 (ttp) cc_final: 0.1954 (mpt) REVERT: R 141 MET cc_start: 0.6817 (ptp) cc_final: 0.6001 (tmt) outliers start: 18 outliers final: 13 residues processed: 115 average time/residue: 1.2319 time to fit residues: 151.8656 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 134 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 0.0270 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.0270 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 392 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.218458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139089 restraints weight = 9361.646| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.52 r_work: 0.3476 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8882 Z= 0.157 Angle : 0.565 15.655 12033 Z= 0.284 Chirality : 0.041 0.170 1374 Planarity : 0.004 0.041 1529 Dihedral : 4.433 58.096 1205 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.92 % Allowed : 21.24 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1091 helix: 1.95 (0.26), residues: 396 sheet: 0.22 (0.32), residues: 269 loop : 0.16 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE R 326 TYR 0.011 0.001 TYR B 289 ARG 0.010 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3398.40 seconds wall clock time: 60 minutes 10.20 seconds (3610.20 seconds total)