Starting phenix.real_space_refine on Sat Apr 6 19:02:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/04_2024/8j21_35941_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/04_2024/8j21_35941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/04_2024/8j21_35941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/04_2024/8j21_35941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/04_2024/8j21_35941_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/04_2024/8j21_35941_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.020 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 58 5.16 5 C 5612 2.51 5 N 1495 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1775 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2188 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BUA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.56 Number of scatterers: 8803 At special positions: 0 Unit cell: (114.4, 109.2, 121.68, 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 58 16.00 O 1638 8.00 N 1495 7.00 C 5612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 169 " distance=2.04 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 34.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 Processing helix chain 'A' and resid 41 through 47 removed outlier: 4.583A pdb=" N ASN A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'C' and resid 4 through 31 removed outlier: 3.536A pdb=" N ALA C 7 " --> pdb=" O THR C 4 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU C 8 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 9 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU C 14 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 28 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 242 through 254 removed outlier: 3.752A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 removed outlier: 3.564A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 310 removed outlier: 3.940A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 350 Processing helix chain 'D' and resid 14 through 45 removed outlier: 4.126A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Proline residue: D 30 - end of helix Processing helix chain 'D' and resid 49 through 72 removed outlier: 3.814A pdb=" N LEU D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Proline residue: D 69 - end of helix Processing helix chain 'D' and resid 86 through 118 removed outlier: 4.133A pdb=" N LEU D 90 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'D' and resid 129 through 153 removed outlier: 3.686A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 151 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 191 removed outlier: 3.540A pdb=" N ILE D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Proline residue: D 183 - end of helix Processing helix chain 'D' and resid 194 through 212 removed outlier: 4.298A pdb=" N ARG D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 207 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL D 208 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 251 Proline residue: D 240 - end of helix removed outlier: 3.594A pdb=" N TYR D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 277 removed outlier: 3.665A pdb=" N VAL D 261 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU D 262 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP D 272 " --> pdb=" O SER D 269 " (cutoff:3.500A) Proline residue: D 273 - end of helix Processing helix chain 'D' and resid 281 through 290 Processing helix chain 'E' and resid 8 through 21 Processing helix chain 'E' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 80 through 84 Processing sheet with id= B, first strand: chain 'A' and resid 122 through 126 removed outlier: 6.010A pdb=" N ASN A 136 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 146 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 157 through 161 removed outlier: 4.151A pdb=" N CYS A 160 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 169 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP A 181 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN A 187 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 209 through 213 removed outlier: 3.555A pdb=" N PHE A 210 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 223 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.426A pdb=" N GLY A 255 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 243 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 253 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 256 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 273 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP A 265 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU A 271 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 295 through 299 removed outlier: 5.036A pdb=" N ASP A 309 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG A 315 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 347 through 350 Processing sheet with id= H, first strand: chain 'B' and resid 41 through 45 Processing sheet with id= I, first strand: chain 'B' and resid 48 through 50 Processing sheet with id= J, first strand: chain 'B' and resid 131 through 137 removed outlier: 3.575A pdb=" N ALA B 87 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG B 76 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TRP B 85 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 193 through 198 Processing sheet with id= L, first strand: chain 'B' and resid 264 through 269 removed outlier: 3.639A pdb=" N ILE B 227 " --> pdb=" O TRP B 214 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU B 216 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU B 225 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 196 through 200 removed outlier: 6.873A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA C 220 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N LEU C 39 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE C 222 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER C 263 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N PHE C 223 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 265 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL C 225 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE C 267 " --> pdb=" O VAL C 225 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 939 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: 2.31 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2840 1.35 - 1.47: 2243 1.47 - 1.59: 3825 1.59 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 8990 Sorted by residual: bond pdb=" CB MET A 72 " pdb=" CG MET A 72 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN B 269 " pdb=" CG GLN B 269 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C TYR B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.08e+00 bond pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 1.803 1.828 -0.025 2.50e-02 1.60e+03 9.75e-01 bond pdb=" CA TRP D 81 " pdb=" CB TRP D 81 " ideal model delta sigma weight residual 1.530 1.516 0.013 1.38e-02 5.25e+03 9.33e-01 ... (remaining 8985 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.80: 133 105.80 - 112.84: 4838 112.84 - 119.88: 2893 119.88 - 126.92: 4208 126.92 - 133.96: 108 Bond angle restraints: 12180 Sorted by residual: angle pdb=" C ALA A 71 " pdb=" N MET A 72 " pdb=" CA MET A 72 " ideal model delta sigma weight residual 122.08 132.69 -10.61 1.84e+00 2.95e-01 3.33e+01 angle pdb=" CA MET A 72 " pdb=" CB MET A 72 " pdb=" CG MET A 72 " ideal model delta sigma weight residual 114.10 124.74 -10.64 2.00e+00 2.50e-01 2.83e+01 angle pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta sigma weight residual 121.80 132.93 -11.13 2.44e+00 1.68e-01 2.08e+01 angle pdb=" CB MET A 72 " pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 112.70 124.42 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CB MET D 79 " pdb=" CG MET D 79 " pdb=" SD MET D 79 " ideal model delta sigma weight residual 112.70 122.13 -9.43 3.00e+00 1.11e-01 9.88e+00 ... (remaining 12175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4438 17.78 - 35.56: 649 35.56 - 53.34: 195 53.34 - 71.13: 27 71.13 - 88.91: 5 Dihedral angle restraints: 5314 sinusoidal: 2064 harmonic: 3250 Sorted by residual: dihedral pdb=" CA ARG A 161 " pdb=" C ARG A 161 " pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 246 " pdb=" C PHE A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta harmonic sigma weight residual 180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU B 272 " pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1035 0.042 - 0.083: 264 0.083 - 0.125: 76 0.125 - 0.166: 5 0.166 - 0.208: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA TYR B 273 " pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CB TYR B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 284 " pdb=" N ILE A 284 " pdb=" C ILE A 284 " pdb=" CB ILE A 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CG LEU D 181 " pdb=" CB LEU D 181 " pdb=" CD1 LEU D 181 " pdb=" CD2 LEU D 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1378 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 273 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO B 274 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 71 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ALA A 71 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA A 71 " 0.017 2.00e-02 2.50e+03 pdb=" N MET A 72 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 140 " 0.013 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" CG TRP D 140 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 140 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 140 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 140 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 140 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 140 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 140 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 140 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 140 " 0.002 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 269 2.69 - 3.24: 8359 3.24 - 3.80: 13999 3.80 - 4.35: 18066 4.35 - 4.90: 30053 Nonbonded interactions: 70746 Sorted by model distance: nonbonded pdb=" O ILE A 69 " pdb=" OG SER A 327 " model vdw 2.140 2.440 nonbonded pdb=" O LEU D 263 " pdb=" OG1 THR D 266 " model vdw 2.172 2.440 nonbonded pdb=" OH TYR B 211 " pdb=" OG SER C 6 " model vdw 2.185 2.440 nonbonded pdb=" OG SER A 342 " pdb=" OD1 ASP A 344 " model vdw 2.193 2.440 nonbonded pdb=" O GLN A 86 " pdb=" OG SER A 109 " model vdw 2.220 2.440 ... (remaining 70741 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=0.01 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 3.970 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.750 Find NCS groups from input model: 0.250 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 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 : 0.002 0.038 8990 Z= 0.150 Angle : 0.618 11.718 12180 Z= 0.310 Chirality : 0.040 0.208 1381 Planarity : 0.004 0.106 1540 Dihedral : 17.794 88.907 3213 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.70 % Favored : 94.76 % Rotamer: Outliers : 0.42 % Allowed : 36.11 % Favored : 63.48 % 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: 0.09 (0.25), residues: 1107 helix: 1.33 (0.27), residues: 388 sheet: 0.68 (0.33), residues: 245 loop : -1.38 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 140 HIS 0.004 0.001 HIS D 245 PHE 0.016 0.001 PHE B 241 TYR 0.019 0.001 TYR D 276 ARG 0.005 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.6730 (mtt90) cc_final: 0.6339 (mtt90) REVERT: A 338 VAL cc_start: 0.8515 (t) cc_final: 0.8208 (p) REVERT: C 198 MET cc_start: 0.7561 (tpp) cc_final: 0.7224 (tpp) outliers start: 4 outliers final: 2 residues processed: 220 average time/residue: 0.2609 time to fit residues: 75.5864 Evaluate side-chains 221 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain D residue 274 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN D 14 HIS E 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8990 Z= 0.259 Angle : 0.624 11.760 12180 Z= 0.313 Chirality : 0.043 0.250 1381 Planarity : 0.005 0.081 1540 Dihedral : 4.666 56.739 1225 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.96 % Favored : 93.41 % Rotamer: Outliers : 7.28 % Allowed : 29.97 % Favored : 62.75 % 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: -0.16 (0.25), residues: 1107 helix: 1.07 (0.26), residues: 399 sheet: 0.34 (0.33), residues: 258 loop : -1.45 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 180 HIS 0.008 0.001 HIS D 245 PHE 0.015 0.002 PHE A 210 TYR 0.016 0.002 TYR D 202 ARG 0.008 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 238 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7255 (p0) REVERT: A 107 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6543 (mtt90) REVERT: A 195 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.8000 (p) REVERT: A 338 VAL cc_start: 0.8616 (t) cc_final: 0.8343 (p) REVERT: B 67 PHE cc_start: 0.8209 (t80) cc_final: 0.7874 (t80) REVERT: B 97 TYR cc_start: 0.7980 (m-80) cc_final: 0.7558 (m-80) REVERT: B 107 THR cc_start: 0.7769 (t) cc_final: 0.7551 (m) REVERT: B 251 THR cc_start: 0.8013 (t) cc_final: 0.7804 (p) REVERT: C 186 GLU cc_start: 0.6384 (mt-10) cc_final: 0.5993 (mt-10) REVERT: D 29 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7856 (mt) REVERT: D 46 ARG cc_start: 0.6614 (OUTLIER) cc_final: 0.6211 (ptt90) REVERT: D 151 TYR cc_start: 0.3693 (p90) cc_final: 0.3099 (p90) outliers start: 70 outliers final: 39 residues processed: 279 average time/residue: 0.2543 time to fit residues: 92.4091 Evaluate side-chains 272 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 229 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 0.0000 chunk 100 optimal weight: 0.4980 chunk 109 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 0.036 8990 Z= 0.213 Angle : 0.581 10.377 12180 Z= 0.290 Chirality : 0.041 0.180 1381 Planarity : 0.004 0.061 1540 Dihedral : 4.245 24.003 1221 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.97 % Favored : 94.49 % Rotamer: Outliers : 6.45 % Allowed : 32.67 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1107 helix: 1.08 (0.26), residues: 399 sheet: 0.35 (0.32), residues: 252 loop : -1.50 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.008 0.001 HIS D 14 PHE 0.020 0.002 PHE C 189 TYR 0.015 0.001 TYR B 273 ARG 0.006 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 226 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.6977 (mtt90) cc_final: 0.6543 (mtt90) REVERT: A 195 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8103 (p) REVERT: A 272 LEU cc_start: 0.7656 (mt) cc_final: 0.7425 (mp) REVERT: A 273 MET cc_start: 0.7723 (ppp) cc_final: 0.7480 (ppp) REVERT: A 338 VAL cc_start: 0.8637 (t) cc_final: 0.8334 (p) REVERT: B 67 PHE cc_start: 0.8297 (t80) cc_final: 0.7952 (t80) REVERT: B 107 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7585 (m) REVERT: C 186 GLU cc_start: 0.6396 (mt-10) cc_final: 0.5970 (mt-10) REVERT: C 240 MET cc_start: 0.3314 (ttp) cc_final: 0.2797 (ttp) REVERT: C 245 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7017 (tm-30) REVERT: D 29 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7801 (mt) REVERT: D 46 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6139 (ptt90) REVERT: D 109 VAL cc_start: 0.8123 (m) cc_final: 0.7765 (p) REVERT: D 112 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: D 151 TYR cc_start: 0.3773 (p90) cc_final: 0.3150 (p90) REVERT: D 275 VAL cc_start: 0.7814 (p) cc_final: 0.7583 (p) outliers start: 62 outliers final: 36 residues processed: 260 average time/residue: 0.2578 time to fit residues: 87.7408 Evaluate side-chains 258 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 270 GLN C 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8990 Z= 0.299 Angle : 0.626 13.119 12180 Z= 0.317 Chirality : 0.043 0.204 1381 Planarity : 0.005 0.064 1540 Dihedral : 4.539 23.694 1221 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.78 % Favored : 93.68 % Rotamer: Outliers : 7.39 % Allowed : 32.26 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1107 helix: 0.92 (0.27), residues: 400 sheet: 0.11 (0.31), residues: 265 loop : -1.58 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 15 HIS 0.018 0.002 HIS D 14 PHE 0.019 0.002 PHE C 189 TYR 0.017 0.002 TYR A 70 ARG 0.008 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 228 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7495 (p0) REVERT: A 107 ARG cc_start: 0.7014 (mtt90) cc_final: 0.6571 (mtt90) REVERT: A 166 ASN cc_start: 0.7607 (t0) cc_final: 0.7322 (t0) REVERT: A 182 ILE cc_start: 0.7563 (mm) cc_final: 0.7337 (mm) REVERT: A 195 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8083 (p) REVERT: A 273 MET cc_start: 0.7769 (ppp) cc_final: 0.7207 (ppp) REVERT: A 338 VAL cc_start: 0.8655 (t) cc_final: 0.8363 (p) REVERT: B 67 PHE cc_start: 0.8327 (t80) cc_final: 0.7923 (t80) REVERT: B 106 PHE cc_start: 0.7799 (m-10) cc_final: 0.7563 (m-80) REVERT: B 107 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7609 (m) REVERT: B 178 MET cc_start: 0.7798 (mmm) cc_final: 0.7501 (mmm) REVERT: C 240 MET cc_start: 0.3420 (ttp) cc_final: 0.2950 (ttp) REVERT: C 245 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7023 (tm-30) REVERT: C 261 ASP cc_start: 0.7466 (t0) cc_final: 0.7146 (t0) REVERT: C 309 ASP cc_start: 0.7426 (m-30) cc_final: 0.7092 (m-30) REVERT: D 29 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7780 (mt) REVERT: D 46 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.6101 (ptt90) REVERT: D 50 VAL cc_start: 0.7953 (OUTLIER) cc_final: 0.7266 (m) REVERT: D 112 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: D 151 TYR cc_start: 0.3708 (p90) cc_final: 0.2907 (p90) REVERT: D 278 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5840 (p90) outliers start: 71 outliers final: 45 residues processed: 275 average time/residue: 0.2406 time to fit residues: 87.1552 Evaluate side-chains 275 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN C 188 HIS C 244 HIS D 14 HIS D 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8990 Z= 0.280 Angle : 0.621 13.122 12180 Z= 0.312 Chirality : 0.043 0.175 1381 Planarity : 0.005 0.062 1540 Dihedral : 4.594 24.314 1221 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.60 % Favored : 93.86 % Rotamer: Outliers : 9.05 % Allowed : 31.01 % Favored : 59.94 % 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: -0.53 (0.25), residues: 1107 helix: 0.82 (0.26), residues: 401 sheet: -0.22 (0.31), residues: 274 loop : -1.53 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 180 HIS 0.024 0.002 HIS C 244 PHE 0.027 0.002 PHE D 173 TYR 0.022 0.002 TYR D 202 ARG 0.006 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 227 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7504 (p0) REVERT: A 107 ARG cc_start: 0.7015 (mtt90) cc_final: 0.6576 (mtt90) REVERT: A 161 ARG cc_start: 0.8017 (mmt180) cc_final: 0.7768 (mmt180) REVERT: A 166 ASN cc_start: 0.7599 (t0) cc_final: 0.7334 (t0) REVERT: A 195 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8088 (p) REVERT: A 273 MET cc_start: 0.7815 (ppp) cc_final: 0.7315 (ppp) REVERT: A 301 ASP cc_start: 0.7007 (m-30) cc_final: 0.6728 (m-30) REVERT: A 338 VAL cc_start: 0.8667 (t) cc_final: 0.8378 (p) REVERT: B 67 PHE cc_start: 0.8367 (t80) cc_final: 0.7879 (t80) REVERT: B 107 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7674 (m) REVERT: B 135 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7934 (t) REVERT: C 240 MET cc_start: 0.3284 (ttp) cc_final: 0.2839 (ttp) REVERT: C 247 MET cc_start: 0.7633 (mmm) cc_final: 0.7268 (mtt) REVERT: C 261 ASP cc_start: 0.7455 (t0) cc_final: 0.7176 (t0) REVERT: C 309 ASP cc_start: 0.7412 (m-30) cc_final: 0.7054 (m-30) REVERT: D 29 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7773 (mt) REVERT: D 46 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6143 (ptt90) REVERT: D 50 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7198 (m) REVERT: D 112 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: D 151 TYR cc_start: 0.3780 (OUTLIER) cc_final: 0.2940 (p90) REVERT: D 278 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5867 (p90) outliers start: 87 outliers final: 58 residues processed: 279 average time/residue: 0.2543 time to fit residues: 92.8118 Evaluate side-chains 295 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 227 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN C 244 HIS D 268 ASN E 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8990 Z= 0.263 Angle : 0.612 14.035 12180 Z= 0.308 Chirality : 0.043 0.254 1381 Planarity : 0.005 0.064 1540 Dihedral : 4.610 26.362 1221 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.51 % Favored : 93.95 % Rotamer: Outliers : 9.47 % Allowed : 30.59 % Favored : 59.94 % 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: -0.56 (0.25), residues: 1107 helix: 0.86 (0.27), residues: 395 sheet: -0.27 (0.31), residues: 273 loop : -1.56 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 180 HIS 0.016 0.001 HIS D 14 PHE 0.021 0.002 PHE B 106 TYR 0.020 0.002 TYR D 202 ARG 0.005 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 222 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7501 (p0) REVERT: A 107 ARG cc_start: 0.6994 (mtt90) cc_final: 0.6575 (mtt90) REVERT: A 161 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7768 (mmt180) REVERT: A 195 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.8101 (p) REVERT: A 273 MET cc_start: 0.7830 (ppp) cc_final: 0.7334 (ppp) REVERT: A 301 ASP cc_start: 0.7003 (m-30) cc_final: 0.6739 (m-30) REVERT: A 338 VAL cc_start: 0.8668 (t) cc_final: 0.8376 (p) REVERT: B 67 PHE cc_start: 0.8379 (t80) cc_final: 0.7850 (t80) REVERT: B 97 TYR cc_start: 0.8010 (m-80) cc_final: 0.7616 (m-80) REVERT: B 107 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7633 (m) REVERT: B 135 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7996 (p) REVERT: C 186 GLU cc_start: 0.6510 (mt-10) cc_final: 0.6302 (mt-10) REVERT: C 197 LYS cc_start: 0.7767 (mmtm) cc_final: 0.7338 (mmtt) REVERT: C 198 MET cc_start: 0.7983 (mtp) cc_final: 0.7762 (ttm) REVERT: C 240 MET cc_start: 0.3255 (ttp) cc_final: 0.2860 (ttp) REVERT: C 245 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7050 (tm-30) REVERT: C 247 MET cc_start: 0.7706 (mmm) cc_final: 0.7343 (mtt) REVERT: C 261 ASP cc_start: 0.7463 (t0) cc_final: 0.7192 (t0) REVERT: C 309 ASP cc_start: 0.7397 (m-30) cc_final: 0.7039 (m-30) REVERT: D 29 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7755 (mt) REVERT: D 46 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6203 (ptt90) REVERT: D 50 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7251 (m) REVERT: D 112 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: D 151 TYR cc_start: 0.3814 (OUTLIER) cc_final: 0.2942 (p90) REVERT: D 207 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7371 (tp) REVERT: D 278 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5867 (p90) outliers start: 91 outliers final: 65 residues processed: 281 average time/residue: 0.2599 time to fit residues: 95.5154 Evaluate side-chains 298 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 222 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN C 244 HIS D 146 HIS D 177 GLN D 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8990 Z= 0.256 Angle : 0.615 13.394 12180 Z= 0.311 Chirality : 0.043 0.212 1381 Planarity : 0.005 0.064 1540 Dihedral : 4.611 26.818 1221 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.42 % Favored : 94.04 % Rotamer: Outliers : 8.53 % Allowed : 31.95 % Favored : 59.52 % 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: -0.60 (0.25), residues: 1107 helix: 0.87 (0.27), residues: 395 sheet: -0.35 (0.31), residues: 275 loop : -1.57 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 180 HIS 0.004 0.001 HIS D 245 PHE 0.030 0.002 PHE D 234 TYR 0.023 0.002 TYR D 202 ARG 0.008 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 229 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7504 (p0) REVERT: A 107 ARG cc_start: 0.6955 (mtt90) cc_final: 0.6524 (mtt90) REVERT: A 161 ARG cc_start: 0.8023 (mmt180) cc_final: 0.7799 (mmt180) REVERT: A 195 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8100 (p) REVERT: A 273 MET cc_start: 0.7846 (ppp) cc_final: 0.7350 (ppp) REVERT: A 301 ASP cc_start: 0.6960 (m-30) cc_final: 0.6695 (m-30) REVERT: A 338 VAL cc_start: 0.8669 (t) cc_final: 0.8385 (p) REVERT: B 97 TYR cc_start: 0.8056 (m-80) cc_final: 0.7682 (m-80) REVERT: B 107 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7688 (m) REVERT: B 135 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7989 (p) REVERT: C 186 GLU cc_start: 0.6515 (mt-10) cc_final: 0.6281 (mt-10) REVERT: C 197 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7549 (mmtt) REVERT: C 198 MET cc_start: 0.7939 (mtp) cc_final: 0.7729 (ttm) REVERT: C 240 MET cc_start: 0.3363 (ttp) cc_final: 0.2971 (ttp) REVERT: C 245 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7074 (tm-30) REVERT: C 247 MET cc_start: 0.7686 (mmm) cc_final: 0.7330 (mtt) REVERT: C 248 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7622 (ptpp) REVERT: C 261 ASP cc_start: 0.7470 (t0) cc_final: 0.7210 (t0) REVERT: C 309 ASP cc_start: 0.7416 (m-30) cc_final: 0.7040 (m-30) REVERT: D 15 TRP cc_start: 0.6852 (OUTLIER) cc_final: 0.6026 (p90) REVERT: D 29 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7752 (mt) REVERT: D 46 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6204 (ptt90) REVERT: D 50 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7265 (m) REVERT: D 112 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: D 151 TYR cc_start: 0.3860 (OUTLIER) cc_final: 0.2971 (p90) REVERT: D 207 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7602 (tp) outliers start: 82 outliers final: 64 residues processed: 278 average time/residue: 0.2535 time to fit residues: 91.8089 Evaluate side-chains 300 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 225 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 0.0980 chunk 102 optimal weight: 0.0030 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 0.0010 overall best weight: 0.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN C 244 HIS D 14 HIS ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8990 Z= 0.155 Angle : 0.580 11.361 12180 Z= 0.290 Chirality : 0.041 0.205 1381 Planarity : 0.004 0.065 1540 Dihedral : 4.318 24.897 1221 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.52 % Favored : 94.94 % Rotamer: Outliers : 6.14 % Allowed : 33.61 % Favored : 60.25 % 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: -0.39 (0.25), residues: 1107 helix: 1.07 (0.27), residues: 391 sheet: -0.05 (0.31), residues: 263 loop : -1.56 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 74 HIS 0.006 0.001 HIS C 244 PHE 0.028 0.001 PHE D 234 TYR 0.018 0.001 TYR D 202 ARG 0.007 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 219 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7282 (p0) REVERT: A 98 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7759 (p) REVERT: A 107 ARG cc_start: 0.6928 (mtt90) cc_final: 0.6499 (mtt90) REVERT: A 273 MET cc_start: 0.7830 (ppp) cc_final: 0.7271 (ppp) REVERT: A 300 TYR cc_start: 0.8525 (m-80) cc_final: 0.8260 (m-80) REVERT: A 315 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7221 (ttm170) REVERT: A 338 VAL cc_start: 0.8629 (t) cc_final: 0.8339 (p) REVERT: B 67 PHE cc_start: 0.8325 (t80) cc_final: 0.7884 (t80) REVERT: B 107 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7620 (m) REVERT: C 240 MET cc_start: 0.3147 (ttp) cc_final: 0.2743 (ttp) REVERT: C 247 MET cc_start: 0.7579 (mmm) cc_final: 0.7300 (mtt) REVERT: C 261 ASP cc_start: 0.7419 (t0) cc_final: 0.7154 (t0) REVERT: C 309 ASP cc_start: 0.7408 (m-30) cc_final: 0.7030 (m-30) REVERT: D 29 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7726 (mt) REVERT: D 46 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6221 (ptt90) REVERT: D 50 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7237 (m) REVERT: D 151 TYR cc_start: 0.3878 (OUTLIER) cc_final: 0.3049 (p90) outliers start: 59 outliers final: 43 residues processed: 255 average time/residue: 0.2861 time to fit residues: 94.3986 Evaluate side-chains 264 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 214 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 0.3980 chunk 64 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: A 270 GLN C 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8990 Z= 0.261 Angle : 0.628 12.465 12180 Z= 0.318 Chirality : 0.043 0.178 1381 Planarity : 0.005 0.065 1540 Dihedral : 4.596 27.166 1221 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.60 % Favored : 93.86 % Rotamer: Outliers : 6.76 % Allowed : 32.78 % Favored : 60.46 % 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: -0.55 (0.25), residues: 1107 helix: 0.86 (0.27), residues: 398 sheet: -0.33 (0.31), residues: 275 loop : -1.51 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 180 HIS 0.005 0.001 HIS D 245 PHE 0.030 0.002 PHE D 234 TYR 0.017 0.002 TYR A 70 ARG 0.007 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 223 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7428 (p0) REVERT: A 57 ARG cc_start: 0.7132 (ptp-170) cc_final: 0.6775 (ptp-170) REVERT: A 107 ARG cc_start: 0.6941 (mtt90) cc_final: 0.6514 (mtt90) REVERT: A 164 ASP cc_start: 0.6323 (m-30) cc_final: 0.6098 (m-30) REVERT: A 226 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: A 250 ASN cc_start: 0.7621 (m-40) cc_final: 0.7407 (m110) REVERT: A 273 MET cc_start: 0.7851 (ppp) cc_final: 0.7318 (ppp) REVERT: A 315 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7229 (ttm170) REVERT: A 338 VAL cc_start: 0.8639 (t) cc_final: 0.8353 (p) REVERT: B 67 PHE cc_start: 0.8358 (t80) cc_final: 0.7860 (t80) REVERT: B 97 TYR cc_start: 0.8004 (m-80) cc_final: 0.7608 (m-80) REVERT: B 135 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7975 (p) REVERT: B 203 LEU cc_start: 0.8332 (mt) cc_final: 0.8114 (mp) REVERT: C 186 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6300 (mt-10) REVERT: C 197 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7616 (mmtt) REVERT: C 198 MET cc_start: 0.7935 (mtp) cc_final: 0.7652 (ttm) REVERT: C 240 MET cc_start: 0.3169 (ttp) cc_final: 0.2798 (ttp) REVERT: C 245 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7025 (tm-30) REVERT: C 247 MET cc_start: 0.7663 (mmm) cc_final: 0.7395 (mtt) REVERT: C 261 ASP cc_start: 0.7480 (t0) cc_final: 0.7259 (t0) REVERT: C 309 ASP cc_start: 0.7477 (m-30) cc_final: 0.7087 (m-30) REVERT: D 15 TRP cc_start: 0.6857 (OUTLIER) cc_final: 0.6198 (p90) REVERT: D 29 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7754 (mt) REVERT: D 151 TYR cc_start: 0.3848 (OUTLIER) cc_final: 0.2954 (p90) REVERT: D 207 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7622 (tp) outliers start: 65 outliers final: 49 residues processed: 263 average time/residue: 0.2528 time to fit residues: 87.0119 Evaluate side-chains 276 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 220 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 0.0050 chunk 26 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN C 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8990 Z= 0.245 Angle : 0.624 12.724 12180 Z= 0.315 Chirality : 0.042 0.175 1381 Planarity : 0.005 0.065 1540 Dihedral : 4.597 27.339 1221 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.60 % Favored : 93.86 % Rotamer: Outliers : 6.66 % Allowed : 32.57 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1107 helix: 0.82 (0.27), residues: 398 sheet: -0.37 (0.31), residues: 269 loop : -1.55 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 140 HIS 0.005 0.001 HIS D 245 PHE 0.023 0.002 PHE D 173 TYR 0.018 0.001 TYR D 202 ARG 0.005 0.000 ARG D 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 215 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7441 (p0) REVERT: A 107 ARG cc_start: 0.6927 (mtt90) cc_final: 0.6529 (mtt90) REVERT: A 163 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7568 (mm) REVERT: A 164 ASP cc_start: 0.6483 (m-30) cc_final: 0.6241 (m-30) REVERT: A 226 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: A 273 MET cc_start: 0.7842 (ppp) cc_final: 0.7351 (ppp) REVERT: A 315 ARG cc_start: 0.7802 (ttm170) cc_final: 0.7268 (ttm170) REVERT: A 338 VAL cc_start: 0.8649 (t) cc_final: 0.8356 (p) REVERT: B 67 PHE cc_start: 0.8350 (t80) cc_final: 0.7860 (t80) REVERT: B 97 TYR cc_start: 0.8041 (m-80) cc_final: 0.7699 (m-80) REVERT: B 135 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7973 (p) REVERT: C 197 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7693 (mmtt) REVERT: C 198 MET cc_start: 0.7957 (mtp) cc_final: 0.7628 (ttm) REVERT: C 240 MET cc_start: 0.3028 (ttp) cc_final: 0.2652 (ttp) REVERT: C 245 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 261 ASP cc_start: 0.7471 (t0) cc_final: 0.7261 (t0) REVERT: C 309 ASP cc_start: 0.7474 (m-30) cc_final: 0.7103 (m-30) REVERT: D 15 TRP cc_start: 0.6850 (OUTLIER) cc_final: 0.6200 (p90) REVERT: D 29 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7747 (mt) REVERT: D 50 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7201 (m) REVERT: D 151 TYR cc_start: 0.3842 (OUTLIER) cc_final: 0.2946 (p90) outliers start: 64 outliers final: 51 residues processed: 250 average time/residue: 0.2608 time to fit residues: 84.8441 Evaluate side-chains 271 residues out of total 961 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 212 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN B 51 GLN C 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127462 restraints weight = 13263.722| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.09 r_work: 0.3419 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8990 Z= 0.293 Angle : 0.654 12.814 12180 Z= 0.332 Chirality : 0.044 0.224 1381 Planarity : 0.005 0.064 1540 Dihedral : 4.787 28.296 1221 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.14 % Favored : 93.32 % Rotamer: Outliers : 7.39 % Allowed : 32.15 % Favored : 60.46 % 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: -0.70 (0.25), residues: 1107 helix: 0.74 (0.27), residues: 398 sheet: -0.23 (0.31), residues: 256 loop : -1.68 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.005 0.001 HIS D 245 PHE 0.031 0.002 PHE D 234 TYR 0.019 0.002 TYR D 202 ARG 0.015 0.001 ARG A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.50 seconds wall clock time: 47 minutes 42.18 seconds (2862.18 seconds total)