Starting phenix.real_space_refine on Wed Feb 14 01:08:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj0_33482/02_2024/8hj0_33482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj0_33482/02_2024/8hj0_33482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj0_33482/02_2024/8hj0_33482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj0_33482/02_2024/8hj0_33482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj0_33482/02_2024/8hj0_33482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hj0_33482/02_2024/8hj0_33482.pdb" } resolution = 3.12 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= 0.005 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 52 5.16 5 C 5250 2.51 5 N 1427 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ASP 49": "OD1" <-> "OD2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 227": "OE1" <-> "OE2" Residue "R PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 308": "OD1" <-> "OD2" Residue "R ARG 317": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8260 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1966 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2297 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 4.72, per 1000 atoms: 0.57 Number of scatterers: 8260 At special positions: 0 Unit cell: (88.4, 102.96, 127.92, 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 52 16.00 O 1531 8.00 N 1427 7.00 C 5250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 122 " - pdb=" SG CYS R 149 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 4.105A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.905A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.821A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.836A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.986A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.887A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.507A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.755A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 26 through 56 removed outlier: 4.382A pdb=" N ILE R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 48 " --> pdb=" O SER R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 61 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.079A pdb=" N TYR R 66 " --> pdb=" O HIS R 62 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 removed outlier: 4.174A pdb=" N SER R 86 " --> pdb=" O CYS R 82 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 133 removed outlier: 4.286A pdb=" N ILE R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 142 through 161 removed outlier: 3.683A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 165 Processing helix chain 'R' and resid 188 through 197 Processing helix chain 'R' and resid 199 through 231 removed outlier: 4.139A pdb=" N ALA R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA R 204 " --> pdb=" O TYR R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 278 Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 282 through 295 Processing helix chain 'R' and resid 298 through 308 removed outlier: 3.747A pdb=" N VAL R 302 " --> pdb=" O PHE R 298 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 322 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.791A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.581A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.517A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.402A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.066A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.791A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.435A 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: 4.004A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.737A 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: 4.030A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 4.136A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1179 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: 2.28 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2702 1.35 - 1.48: 2214 1.48 - 1.62: 3457 1.62 - 1.75: 0 1.75 - 1.88: 70 Bond restraints: 8443 Sorted by residual: bond pdb=" CB CYS R 149 " pdb=" SG CYS R 149 " ideal model delta sigma weight residual 1.808 1.877 -0.069 3.30e-02 9.18e+02 4.38e+00 bond pdb=" CA ALA B 328 " pdb=" CB ALA B 328 " ideal model delta sigma weight residual 1.526 1.494 0.032 1.70e-02 3.46e+03 3.61e+00 bond pdb=" C VAL R 84 " pdb=" N PRO R 85 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.46e+00 bond pdb=" C ASN R 300 " pdb=" N PRO R 301 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.43e+00 bond pdb=" CB ASP R 126 " pdb=" CG ASP R 126 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.38e+00 ... (remaining 8438 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.32: 93 104.32 - 111.82: 3851 111.82 - 119.33: 2980 119.33 - 126.84: 4405 126.84 - 134.35: 120 Bond angle restraints: 11449 Sorted by residual: angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C GLU R 97 " pdb=" N GLU R 98 " pdb=" CA GLU R 98 " ideal model delta sigma weight residual 121.54 130.46 -8.92 1.91e+00 2.74e-01 2.18e+01 angle pdb=" CA ASP R 126 " pdb=" CB ASP R 126 " pdb=" CG ASP R 126 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.00e+00 1.00e+00 1.72e+01 angle pdb=" CB ARG R 256 " pdb=" CG ARG R 256 " pdb=" CD ARG R 256 " ideal model delta sigma weight residual 111.30 119.61 -8.31 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 110.48 105.27 5.21 1.48e+00 4.57e-01 1.24e+01 ... (remaining 11444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4488 17.97 - 35.94: 410 35.94 - 53.91: 80 53.91 - 71.88: 13 71.88 - 89.84: 11 Dihedral angle restraints: 5002 sinusoidal: 1963 harmonic: 3039 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 14.33 78.67 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS R 122 " pdb=" SG CYS R 122 " pdb=" SG CYS R 149 " pdb=" CB CYS R 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.02 -66.02 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CA SER R 307 " pdb=" C SER R 307 " pdb=" N ASP R 308 " pdb=" CA ASP R 308 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1091 0.078 - 0.155: 171 0.155 - 0.232: 21 0.232 - 0.310: 1 0.310 - 0.387: 3 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB ILE B 269 " pdb=" CA ILE B 269 " pdb=" CG1 ILE B 269 " pdb=" CG2 ILE B 269 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1284 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO N 14 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 215 " -0.024 2.00e-02 2.50e+03 2.69e-02 1.26e+01 pdb=" CG PHE R 215 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE R 215 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE R 215 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE R 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 215 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 215 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 124 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C SER R 124 " 0.050 2.00e-02 2.50e+03 pdb=" O SER R 124 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE R 125 " -0.017 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1882 2.78 - 3.31: 7840 3.31 - 3.84: 14430 3.84 - 4.37: 17211 4.37 - 4.90: 28894 Nonbonded interactions: 70257 Sorted by model distance: nonbonded pdb=" O VAL R 83 " pdb=" OG SER R 86 " model vdw 2.254 2.440 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.256 2.440 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.259 2.440 nonbonded pdb=" O TRP R 180 " pdb=" OG SER R 184 " model vdw 2.259 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.266 2.440 ... (remaining 70252 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.960 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 24.310 Find NCS groups from input model: 0.200 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 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 : 0.006 0.069 8443 Z= 0.364 Angle : 1.070 11.028 11449 Z= 0.598 Chirality : 0.058 0.387 1287 Planarity : 0.008 0.117 1457 Dihedral : 14.888 89.844 3024 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.89 (0.24), residues: 1029 helix: -0.90 (0.24), residues: 401 sheet: -0.79 (0.33), residues: 214 loop : -1.73 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP R 180 HIS 0.015 0.002 HIS A 220 PHE 0.063 0.004 PHE R 215 TYR 0.021 0.003 TYR A 348 ARG 0.026 0.002 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 111 TYR cc_start: 0.6383 (m-80) cc_final: 0.6142 (m-80) REVERT: G 21 MET cc_start: 0.4214 (mmm) cc_final: 0.2584 (mtm) REVERT: R 31 GLU cc_start: 0.5584 (mm-30) cc_final: 0.4817 (mm-30) REVERT: R 152 LEU cc_start: 0.6932 (mt) cc_final: 0.6605 (mp) REVERT: R 287 PHE cc_start: 0.5795 (t80) cc_final: 0.5311 (t80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2373 time to fit residues: 62.4201 Evaluate side-chains 154 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 261 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN N 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8443 Z= 0.189 Angle : 0.577 5.684 11449 Z= 0.308 Chirality : 0.043 0.142 1287 Planarity : 0.005 0.083 1457 Dihedral : 5.251 19.527 1136 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.55 % Allowed : 9.30 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.25), residues: 1029 helix: 0.32 (0.25), residues: 408 sheet: -0.72 (0.33), residues: 217 loop : -1.49 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.009 0.001 HIS B 91 PHE 0.016 0.002 PHE R 272 TYR 0.010 0.001 TYR A 329 ARG 0.008 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 1.004 Fit side-chains REVERT: A 60 MET cc_start: 0.6838 (mpp) cc_final: 0.6540 (mpp) REVERT: B 111 TYR cc_start: 0.6316 (m-80) cc_final: 0.6056 (m-80) REVERT: B 118 ASP cc_start: 0.5922 (t70) cc_final: 0.5429 (t70) REVERT: G 21 MET cc_start: 0.4292 (mmm) cc_final: 0.2540 (mtt) REVERT: R 152 LEU cc_start: 0.7024 (mt) cc_final: 0.6539 (mp) REVERT: R 194 PHE cc_start: 0.6458 (m-80) cc_final: 0.6084 (m-80) outliers start: 14 outliers final: 8 residues processed: 182 average time/residue: 0.2589 time to fit residues: 61.0532 Evaluate side-chains 159 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 123 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 62 optimal weight: 0.0070 chunk 25 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 361 ASN B 35 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8443 Z= 0.180 Angle : 0.541 5.818 11449 Z= 0.290 Chirality : 0.042 0.171 1287 Planarity : 0.004 0.068 1457 Dihedral : 4.859 18.629 1136 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.33 % Allowed : 12.85 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1029 helix: 0.79 (0.26), residues: 410 sheet: -0.66 (0.32), residues: 228 loop : -1.18 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS B 91 PHE 0.016 0.002 PHE R 287 TYR 0.012 0.001 TYR B 264 ARG 0.005 0.000 ARG R 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 0.716 Fit side-chains REVERT: A 60 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6487 (mpp) REVERT: A 325 THR cc_start: 0.8084 (m) cc_final: 0.7828 (m) REVERT: B 59 TYR cc_start: 0.5618 (t80) cc_final: 0.5375 (t80) REVERT: B 111 TYR cc_start: 0.6289 (m-80) cc_final: 0.6011 (m-80) REVERT: B 118 ASP cc_start: 0.5993 (t70) cc_final: 0.5529 (t70) REVERT: B 247 ASP cc_start: 0.7350 (p0) cc_final: 0.7004 (p0) REVERT: B 275 SER cc_start: 0.7968 (t) cc_final: 0.7310 (m) REVERT: G 21 MET cc_start: 0.4202 (mmm) cc_final: 0.2570 (mtt) REVERT: R 152 LEU cc_start: 0.7066 (mt) cc_final: 0.6538 (mp) outliers start: 21 outliers final: 16 residues processed: 179 average time/residue: 0.2484 time to fit residues: 57.7377 Evaluate side-chains 175 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 236 GLN A 361 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 237 ASN R 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8443 Z= 0.173 Angle : 0.532 5.759 11449 Z= 0.284 Chirality : 0.042 0.236 1287 Planarity : 0.004 0.051 1457 Dihedral : 4.650 18.467 1136 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.32 % Allowed : 13.40 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1029 helix: 1.14 (0.26), residues: 410 sheet: -0.63 (0.32), residues: 229 loop : -1.04 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS B 91 PHE 0.020 0.002 PHE R 194 TYR 0.011 0.001 TYR B 264 ARG 0.006 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 325 THR cc_start: 0.8061 (m) cc_final: 0.7809 (m) REVERT: A 346 ARG cc_start: 0.6871 (mpp80) cc_final: 0.6640 (mpp-170) REVERT: B 43 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7292 (mp) REVERT: B 111 TYR cc_start: 0.6280 (m-80) cc_final: 0.6005 (m-80) REVERT: B 118 ASP cc_start: 0.6073 (t70) cc_final: 0.5705 (t70) REVERT: B 247 ASP cc_start: 0.7334 (p0) cc_final: 0.6976 (p0) REVERT: B 275 SER cc_start: 0.7959 (t) cc_final: 0.7345 (m) REVERT: G 21 MET cc_start: 0.4192 (mmm) cc_final: 0.2730 (mtt) REVERT: N 72 ARG cc_start: 0.7052 (ptm160) cc_final: 0.6848 (ptm160) outliers start: 30 outliers final: 23 residues processed: 185 average time/residue: 0.2440 time to fit residues: 58.9122 Evaluate side-chains 184 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8443 Z= 0.203 Angle : 0.565 9.604 11449 Z= 0.296 Chirality : 0.043 0.236 1287 Planarity : 0.004 0.048 1457 Dihedral : 4.644 18.143 1136 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.65 % Allowed : 15.06 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1029 helix: 1.31 (0.25), residues: 411 sheet: -0.61 (0.32), residues: 229 loop : -0.94 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 271 HIS 0.007 0.001 HIS B 91 PHE 0.024 0.002 PHE R 194 TYR 0.011 0.001 TYR B 264 ARG 0.007 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6363 (mp10) cc_final: 0.6115 (mp10) REVERT: B 43 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7413 (mp) REVERT: B 111 TYR cc_start: 0.6322 (m-80) cc_final: 0.6006 (m-80) REVERT: B 118 ASP cc_start: 0.6192 (t70) cc_final: 0.5810 (t70) REVERT: B 247 ASP cc_start: 0.7351 (p0) cc_final: 0.7002 (p0) REVERT: B 275 SER cc_start: 0.8053 (t) cc_final: 0.7373 (m) REVERT: G 21 MET cc_start: 0.4184 (mmm) cc_final: 0.2663 (mtt) outliers start: 33 outliers final: 28 residues processed: 187 average time/residue: 0.2413 time to fit residues: 58.9927 Evaluate side-chains 192 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 307 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8443 Z= 0.174 Angle : 0.542 7.811 11449 Z= 0.283 Chirality : 0.042 0.232 1287 Planarity : 0.004 0.047 1457 Dihedral : 4.487 17.354 1136 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.54 % Allowed : 16.17 % Favored : 80.29 % 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: 0.21 (0.26), residues: 1029 helix: 1.54 (0.26), residues: 411 sheet: -0.49 (0.32), residues: 228 loop : -0.92 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 271 HIS 0.008 0.001 HIS B 91 PHE 0.025 0.001 PHE R 194 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 171 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6394 (mt0) cc_final: 0.6132 (mp10) REVERT: A 325 THR cc_start: 0.8072 (m) cc_final: 0.7822 (m) REVERT: B 43 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7416 (mp) REVERT: B 111 TYR cc_start: 0.6312 (m-80) cc_final: 0.5944 (m-80) REVERT: B 118 ASP cc_start: 0.6118 (t70) cc_final: 0.5725 (t70) REVERT: B 247 ASP cc_start: 0.7331 (p0) cc_final: 0.7007 (p0) REVERT: B 252 LEU cc_start: 0.7080 (tp) cc_final: 0.6880 (tp) REVERT: B 275 SER cc_start: 0.8013 (t) cc_final: 0.7393 (m) REVERT: B 325 MET cc_start: 0.7285 (mmt) cc_final: 0.7079 (mmt) REVERT: G 21 MET cc_start: 0.4369 (mmm) cc_final: 0.2877 (mtt) REVERT: R 178 PHE cc_start: 0.4427 (t80) cc_final: 0.4035 (t80) outliers start: 32 outliers final: 26 residues processed: 185 average time/residue: 0.2506 time to fit residues: 61.5400 Evaluate side-chains 191 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 307 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.0570 chunk 58 optimal weight: 4.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8443 Z= 0.168 Angle : 0.528 7.654 11449 Z= 0.277 Chirality : 0.042 0.211 1287 Planarity : 0.004 0.049 1457 Dihedral : 4.396 17.120 1136 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.88 % Allowed : 16.28 % Favored : 79.84 % 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: 0.32 (0.26), residues: 1029 helix: 1.69 (0.26), residues: 412 sheet: -0.44 (0.32), residues: 228 loop : -0.95 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 271 HIS 0.007 0.001 HIS B 91 PHE 0.024 0.001 PHE R 194 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6269 (mt0) cc_final: 0.6001 (mp10) REVERT: A 325 THR cc_start: 0.8057 (m) cc_final: 0.7811 (m) REVERT: B 43 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7360 (mp) REVERT: B 111 TYR cc_start: 0.6319 (m-80) cc_final: 0.5960 (m-80) REVERT: B 118 ASP cc_start: 0.6079 (t70) cc_final: 0.5713 (t70) REVERT: B 252 LEU cc_start: 0.7042 (tp) cc_final: 0.6575 (tp) REVERT: B 275 SER cc_start: 0.7988 (t) cc_final: 0.7386 (m) REVERT: G 21 MET cc_start: 0.4342 (mmm) cc_final: 0.2895 (mtt) REVERT: R 178 PHE cc_start: 0.4553 (t80) cc_final: 0.4128 (t80) outliers start: 35 outliers final: 27 residues processed: 190 average time/residue: 0.2405 time to fit residues: 60.1352 Evaluate side-chains 189 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 307 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8443 Z= 0.183 Angle : 0.546 7.444 11449 Z= 0.288 Chirality : 0.043 0.220 1287 Planarity : 0.004 0.050 1457 Dihedral : 4.424 17.292 1136 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.21 % Allowed : 16.83 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1029 helix: 1.69 (0.26), residues: 410 sheet: -0.34 (0.33), residues: 226 loop : -0.92 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.008 0.001 HIS B 91 PHE 0.027 0.002 PHE R 194 TYR 0.010 0.001 TYR A 308 ARG 0.009 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6272 (mt0) cc_final: 0.6001 (mp10) REVERT: A 325 THR cc_start: 0.8076 (m) cc_final: 0.7827 (m) REVERT: B 43 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7382 (mp) REVERT: B 111 TYR cc_start: 0.6344 (m-80) cc_final: 0.5943 (m-80) REVERT: B 118 ASP cc_start: 0.6089 (OUTLIER) cc_final: 0.5726 (t70) REVERT: B 252 LEU cc_start: 0.7117 (tp) cc_final: 0.6589 (tp) REVERT: B 262 MET cc_start: 0.6174 (mtm) cc_final: 0.5862 (mmt) REVERT: B 275 SER cc_start: 0.7995 (t) cc_final: 0.7395 (m) REVERT: G 21 MET cc_start: 0.4365 (mmm) cc_final: 0.2885 (mtt) REVERT: G 28 ILE cc_start: 0.6944 (mp) cc_final: 0.6427 (mm) REVERT: R 101 THR cc_start: 0.6475 (t) cc_final: 0.6221 (t) REVERT: R 178 PHE cc_start: 0.4457 (t80) cc_final: 0.4042 (t80) outliers start: 38 outliers final: 32 residues processed: 187 average time/residue: 0.2263 time to fit residues: 56.5003 Evaluate side-chains 196 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 307 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8443 Z= 0.203 Angle : 0.561 8.341 11449 Z= 0.294 Chirality : 0.043 0.222 1287 Planarity : 0.004 0.050 1457 Dihedral : 4.477 17.603 1136 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.21 % Allowed : 16.83 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1029 helix: 1.56 (0.26), residues: 410 sheet: -0.33 (0.33), residues: 226 loop : -0.89 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.009 0.001 HIS B 91 PHE 0.030 0.002 PHE R 194 TYR 0.010 0.001 TYR N 95 ARG 0.009 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6262 (mt0) cc_final: 0.5880 (mp10) REVERT: A 325 THR cc_start: 0.8189 (m) cc_final: 0.7911 (m) REVERT: B 43 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7493 (mp) REVERT: B 111 TYR cc_start: 0.6348 (m-80) cc_final: 0.5978 (m-80) REVERT: B 118 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5787 (t70) REVERT: B 252 LEU cc_start: 0.7142 (tp) cc_final: 0.6616 (tp) REVERT: B 258 ASP cc_start: 0.7409 (t0) cc_final: 0.7186 (t0) REVERT: B 275 SER cc_start: 0.8030 (t) cc_final: 0.7422 (m) REVERT: G 28 ILE cc_start: 0.7094 (mp) cc_final: 0.6561 (mm) REVERT: R 178 PHE cc_start: 0.4440 (t80) cc_final: 0.4041 (t80) outliers start: 38 outliers final: 33 residues processed: 182 average time/residue: 0.2275 time to fit residues: 55.0628 Evaluate side-chains 190 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 307 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 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 0.052 8443 Z= 0.185 Angle : 0.560 7.769 11449 Z= 0.291 Chirality : 0.043 0.183 1287 Planarity : 0.004 0.051 1457 Dihedral : 4.424 17.304 1136 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.99 % Allowed : 17.17 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1029 helix: 1.62 (0.26), residues: 411 sheet: -0.29 (0.33), residues: 225 loop : -0.90 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS B 91 PHE 0.030 0.002 PHE R 194 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6909 (mtt180) cc_final: 0.6544 (mtt90) REVERT: A 59 GLN cc_start: 0.5987 (mt0) cc_final: 0.5748 (mp10) REVERT: A 325 THR cc_start: 0.8168 (m) cc_final: 0.7900 (m) REVERT: B 43 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7502 (mp) REVERT: B 111 TYR cc_start: 0.6342 (m-80) cc_final: 0.5928 (m-80) REVERT: B 118 ASP cc_start: 0.6069 (OUTLIER) cc_final: 0.5733 (t70) REVERT: B 275 SER cc_start: 0.7995 (t) cc_final: 0.7396 (m) REVERT: G 28 ILE cc_start: 0.6956 (mp) cc_final: 0.6429 (mm) REVERT: R 178 PHE cc_start: 0.4420 (t80) cc_final: 0.4035 (t80) outliers start: 36 outliers final: 32 residues processed: 178 average time/residue: 0.2331 time to fit residues: 55.3445 Evaluate side-chains 188 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 307 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.232974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.199221 restraints weight = 8718.392| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.81 r_work: 0.4098 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8443 Z= 0.162 Angle : 0.554 13.095 11449 Z= 0.286 Chirality : 0.043 0.207 1287 Planarity : 0.004 0.051 1457 Dihedral : 4.321 17.028 1136 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.77 % Allowed : 18.05 % Favored : 78.18 % 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: 0.44 (0.27), residues: 1029 helix: 1.72 (0.26), residues: 411 sheet: -0.24 (0.33), residues: 226 loop : -0.88 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.008 0.001 HIS B 91 PHE 0.031 0.001 PHE R 287 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG B 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.11 seconds wall clock time: 40 minutes 48.73 seconds (2448.73 seconds total)