Starting phenix.real_space_refine on Thu Mar 14 14:04:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3j_7039/03_2024/6b3j_7039.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3j_7039/03_2024/6b3j_7039.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/6b3j_7039/03_2024/6b3j_7039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3j_7039/03_2024/6b3j_7039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3j_7039/03_2024/6b3j_7039.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3j_7039/03_2024/6b3j_7039.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= 0.008 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 54 5.16 5 C 5758 2.51 5 N 1560 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9034 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3134 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 364} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 254 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1654 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain breaks: 4 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 4.36, per 1000 atoms: 0.48 Number of scatterers: 9034 At special positions: 0 Unit cell: (82.68, 177.02, 98.58, 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 54 16.00 O 1662 8.00 N 1560 7.00 C 5758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 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: 3.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 44.3% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 91 through 95 removed outlier: 3.577A pdb=" N SER R 94 " --> pdb=" O TRP R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 170 removed outlier: 4.006A pdb=" N ARG R 170 " --> pdb=" O LEU R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.535A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 211 Processing helix chain 'R' and resid 213 through 223 Processing helix chain 'R' and resid 225 through 257 removed outlier: 3.722A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 292 Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 296 through 300 removed outlier: 3.785A pdb=" N ARG R 299 " --> pdb=" O CYS R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.640A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 361 through 370 Processing helix chain 'R' and resid 372 through 376 removed outlier: 3.612A pdb=" N ARG R 376 " --> pdb=" O GLU R 373 " (cutoff:3.500A) Processing helix chain 'R' and resid 379 through 405 removed outlier: 4.307A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 Processing helix chain 'P' and resid 2 through 31 Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.126A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 4.112A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.832A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.987A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.734A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.632A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.759A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.532A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.584A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 83 through 84 removed outlier: 4.107A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL R 100 " --> pdb=" O VAL R 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.602A pdb=" N VAL A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.608A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.354A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.724A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.892A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.583A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.792A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 7.111A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1380 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: 2.79 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2888 1.34 - 1.46: 2116 1.46 - 1.58: 4163 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 9240 Sorted by residual: bond pdb=" CB TRP B 169 " pdb=" CG TRP B 169 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.30e+00 bond pdb=" C VAL R 276 " pdb=" N PRO R 277 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.36e-02 5.41e+03 3.30e+00 bond pdb=" N LYS R 113 " pdb=" CA LYS R 113 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.16e+00 bond pdb=" N ILE R 357 " pdb=" CA ILE R 357 " ideal model delta sigma weight residual 1.464 1.484 -0.020 1.23e-02 6.61e+03 2.53e+00 bond pdb=" CB MET P 15 " pdb=" CG MET P 15 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.35e+00 ... (remaining 9235 not shown) Histogram of bond angle deviations from ideal: 97.14 - 104.83: 117 104.83 - 112.51: 4602 112.51 - 120.20: 3787 120.20 - 127.88: 3912 127.88 - 135.57: 106 Bond angle restraints: 12524 Sorted by residual: angle pdb=" C LYS N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 121.54 132.25 -10.71 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C GLU A 330 " pdb=" N ASP A 331 " pdb=" CA ASP A 331 " ideal model delta sigma weight residual 121.59 135.57 -13.98 3.54e+00 7.98e-02 1.56e+01 angle pdb=" N GLY R 168 " pdb=" CA GLY R 168 " pdb=" C GLY R 168 " ideal model delta sigma weight residual 112.73 117.15 -4.42 1.20e+00 6.94e-01 1.35e+01 ... (remaining 12519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 5186 15.66 - 31.33: 216 31.33 - 46.99: 52 46.99 - 62.65: 3 62.65 - 78.32: 7 Dihedral angle restraints: 5464 sinusoidal: 2178 harmonic: 3286 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 171.32 -78.32 1 1.00e+01 1.00e-02 7.66e+01 dihedral pdb=" CA ALA R 57 " pdb=" C ALA R 57 " pdb=" N THR R 58 " pdb=" CA THR R 58 " ideal model delta harmonic sigma weight residual 180.00 144.49 35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CA SER R 261 " pdb=" C SER R 261 " pdb=" N GLU R 262 " pdb=" CA GLU R 262 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1068 0.069 - 0.138: 264 0.138 - 0.207: 37 0.207 - 0.276: 5 0.276 - 0.345: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CB VAL R 276 " pdb=" CA VAL R 276 " pdb=" CG1 VAL R 276 " pdb=" CG2 VAL R 276 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE R 317 " pdb=" CA ILE R 317 " pdb=" CG1 ILE R 317 " pdb=" CG2 ILE R 317 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1373 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 272 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ILE R 272 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE R 272 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY R 273 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 361 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.025 2.00e-02 2.50e+03 1.96e-02 7.65e+00 pdb=" CG TYR B 105 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.001 2.00e-02 2.50e+03 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1328 2.76 - 3.30: 8363 3.30 - 3.83: 14711 3.83 - 4.37: 16344 4.37 - 4.90: 29559 Nonbonded interactions: 70305 Sorted by model distance: nonbonded pdb=" OG1 THR N 91 " pdb=" O VAL N 124 " model vdw 2.229 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR R 105 " pdb=" O LEU R 109 " model vdw 2.276 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.300 2.440 ... (remaining 70300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 2.140 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 24.900 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.007 0.075 9240 Z= 0.452 Angle : 1.004 13.976 12524 Z= 0.568 Chirality : 0.061 0.345 1376 Planarity : 0.007 0.089 1597 Dihedral : 9.888 77.618 3320 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1105 helix: 2.60 (0.22), residues: 451 sheet: 0.58 (0.37), residues: 196 loop : -2.12 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP R 72 HIS 0.010 0.002 HIS R 171 PHE 0.026 0.003 PHE R 367 TYR 0.048 0.004 TYR B 105 ARG 0.010 0.001 ARG R 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4130 (p0) cc_final: 0.3885 (m-30) REVERT: R 123 LEU cc_start: 0.4851 (pp) cc_final: 0.4611 (tp) REVERT: R 127 GLU cc_start: 0.6915 (tp30) cc_final: 0.6556 (mt-10) REVERT: R 182 ASN cc_start: 0.8973 (m-40) cc_final: 0.8719 (m110) REVERT: R 211 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7910 (tt0) REVERT: R 242 TYR cc_start: 0.8440 (m-80) cc_final: 0.8026 (m-80) REVERT: R 305 TYR cc_start: 0.7486 (m-10) cc_final: 0.7153 (m-10) REVERT: R 351 LYS cc_start: 0.8633 (tttt) cc_final: 0.8249 (mmtt) REVERT: R 367 PHE cc_start: 0.8126 (m-80) cc_final: 0.7925 (m-10) REVERT: R 370 VAL cc_start: 0.7561 (t) cc_final: 0.7265 (t) REVERT: R 393 PHE cc_start: 0.8134 (m-10) cc_final: 0.7760 (m-10) REVERT: R 404 PHE cc_start: 0.4434 (t80) cc_final: 0.3359 (m-80) REVERT: R 408 GLU cc_start: 0.8503 (pt0) cc_final: 0.8124 (pt0) REVERT: P 21 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8192 (mmm-85) REVERT: A 286 SER cc_start: 0.9165 (m) cc_final: 0.8717 (p) REVERT: B 23 LYS cc_start: 0.8236 (tttp) cc_final: 0.7512 (mmtt) REVERT: B 46 ARG cc_start: 0.7053 (tpt-90) cc_final: 0.6555 (mtp-110) REVERT: B 71 VAL cc_start: 0.8702 (t) cc_final: 0.8438 (p) REVERT: B 82 TRP cc_start: 0.8855 (m100) cc_final: 0.8629 (m100) REVERT: B 111 TYR cc_start: 0.8655 (m-80) cc_final: 0.8453 (m-80) REVERT: B 154 ASP cc_start: 0.7964 (m-30) cc_final: 0.7611 (t0) REVERT: B 189 SER cc_start: 0.9163 (t) cc_final: 0.8883 (p) REVERT: B 191 SER cc_start: 0.8693 (t) cc_final: 0.8425 (p) REVERT: B 217 MET cc_start: 0.7812 (ptp) cc_final: 0.7320 (tpt) REVERT: G 14 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7309 (tttp) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.2814 time to fit residues: 89.5084 Evaluate side-chains 124 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 115 ASN R 263 GLN R 407 ASN B 6 GLN B 155 ASN B 266 HIS G 18 GLN G 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9240 Z= 0.221 Angle : 0.622 8.681 12524 Z= 0.334 Chirality : 0.043 0.176 1376 Planarity : 0.005 0.054 1597 Dihedral : 5.535 50.685 1233 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.27 % Allowed : 8.96 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1105 helix: 2.88 (0.23), residues: 454 sheet: 0.50 (0.36), residues: 197 loop : -1.80 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 33 HIS 0.005 0.001 HIS G 44 PHE 0.028 0.002 PHE R 230 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.028 Fit side-chains REVERT: R 67 ASP cc_start: 0.4476 (OUTLIER) cc_final: 0.3766 (m-30) REVERT: R 123 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4781 (tp) REVERT: R 127 GLU cc_start: 0.6670 (tp30) cc_final: 0.6230 (mt-10) REVERT: R 267 ARG cc_start: 0.6559 (mmm-85) cc_final: 0.6291 (mtp180) REVERT: R 305 TYR cc_start: 0.7477 (m-10) cc_final: 0.7162 (m-10) REVERT: R 354 LEU cc_start: 0.8182 (mt) cc_final: 0.7898 (tt) REVERT: R 393 PHE cc_start: 0.7981 (m-10) cc_final: 0.7779 (m-10) REVERT: R 404 PHE cc_start: 0.4231 (t80) cc_final: 0.3454 (m-80) REVERT: A 286 SER cc_start: 0.9155 (m) cc_final: 0.8649 (p) REVERT: B 23 LYS cc_start: 0.8269 (tttp) cc_final: 0.7546 (mmtt) REVERT: B 46 ARG cc_start: 0.6830 (tpt-90) cc_final: 0.6406 (mmm160) REVERT: B 82 TRP cc_start: 0.8740 (m100) cc_final: 0.8394 (m100) REVERT: B 118 ASP cc_start: 0.8073 (p0) cc_final: 0.7736 (t0) REVERT: B 154 ASP cc_start: 0.7831 (m-30) cc_final: 0.7531 (t0) REVERT: B 189 SER cc_start: 0.9129 (t) cc_final: 0.8753 (p) REVERT: B 191 SER cc_start: 0.8261 (t) cc_final: 0.8000 (t) REVERT: B 217 MET cc_start: 0.7867 (ptp) cc_final: 0.7637 (tpt) REVERT: B 270 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (pp) REVERT: G 14 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7271 (tttp) outliers start: 22 outliers final: 14 residues processed: 153 average time/residue: 0.2099 time to fit residues: 44.4257 Evaluate side-chains 130 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9240 Z= 0.154 Angle : 0.535 7.857 12524 Z= 0.287 Chirality : 0.041 0.165 1376 Planarity : 0.004 0.062 1597 Dihedral : 4.987 42.768 1233 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 10.30 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1105 helix: 3.01 (0.24), residues: 449 sheet: 0.49 (0.36), residues: 197 loop : -1.49 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 243 HIS 0.003 0.001 HIS R 99 PHE 0.028 0.001 PHE R 385 TYR 0.019 0.001 TYR N 60 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: R 120 TRP cc_start: 0.5774 (t60) cc_final: 0.5372 (t60) REVERT: R 127 GLU cc_start: 0.6519 (tp30) cc_final: 0.5926 (mt-10) REVERT: R 262 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7856 (mm-30) REVERT: R 267 ARG cc_start: 0.6492 (mmm-85) cc_final: 0.6240 (mtp180) REVERT: R 305 TYR cc_start: 0.7749 (m-10) cc_final: 0.7423 (m-10) REVERT: R 404 PHE cc_start: 0.4269 (t80) cc_final: 0.3494 (m-80) REVERT: A 27 GLU cc_start: 0.7344 (pp20) cc_final: 0.7100 (pp20) REVERT: A 286 SER cc_start: 0.9140 (m) cc_final: 0.8638 (p) REVERT: A 386 MET cc_start: 0.8930 (ttp) cc_final: 0.8697 (tmm) REVERT: B 23 LYS cc_start: 0.8267 (tttp) cc_final: 0.7555 (mmtt) REVERT: B 46 ARG cc_start: 0.6898 (tpt-90) cc_final: 0.6475 (mmm160) REVERT: B 71 VAL cc_start: 0.8630 (t) cc_final: 0.8427 (p) REVERT: B 82 TRP cc_start: 0.8710 (m100) cc_final: 0.8361 (m100) REVERT: B 154 ASP cc_start: 0.7943 (m-30) cc_final: 0.7574 (t0) REVERT: B 170 ASP cc_start: 0.6791 (t0) cc_final: 0.6388 (t0) REVERT: B 189 SER cc_start: 0.9090 (t) cc_final: 0.8718 (p) REVERT: B 191 SER cc_start: 0.8247 (t) cc_final: 0.7998 (t) REVERT: B 217 MET cc_start: 0.7899 (ptp) cc_final: 0.7667 (tpt) REVERT: G 14 LYS cc_start: 0.7726 (mmmt) cc_final: 0.7333 (tttp) outliers start: 31 outliers final: 20 residues processed: 158 average time/residue: 0.1854 time to fit residues: 42.3369 Evaluate side-chains 144 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9240 Z= 0.148 Angle : 0.512 6.893 12524 Z= 0.274 Chirality : 0.040 0.153 1376 Planarity : 0.004 0.056 1597 Dihedral : 4.759 38.826 1233 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.78 % Allowed : 11.95 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1105 helix: 3.02 (0.24), residues: 448 sheet: 0.44 (0.36), residues: 197 loop : -1.30 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 33 HIS 0.003 0.001 HIS R 99 PHE 0.020 0.001 PHE R 385 TYR 0.014 0.001 TYR N 60 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4387 (OUTLIER) cc_final: 0.3759 (m-30) REVERT: R 123 LEU cc_start: 0.5059 (OUTLIER) cc_final: 0.4720 (tp) REVERT: R 127 GLU cc_start: 0.6437 (tp30) cc_final: 0.6084 (mt-10) REVERT: R 139 GLU cc_start: 0.7284 (tt0) cc_final: 0.6382 (pm20) REVERT: R 267 ARG cc_start: 0.6442 (mmm-85) cc_final: 0.6224 (mtp180) REVERT: R 305 TYR cc_start: 0.7775 (m-10) cc_final: 0.7468 (m-10) REVERT: R 404 PHE cc_start: 0.4357 (t80) cc_final: 0.3458 (m-80) REVERT: A 27 GLU cc_start: 0.7444 (pp20) cc_final: 0.7182 (pp20) REVERT: A 286 SER cc_start: 0.9141 (m) cc_final: 0.8641 (p) REVERT: A 386 MET cc_start: 0.8931 (ttp) cc_final: 0.8706 (tmm) REVERT: B 23 LYS cc_start: 0.8285 (tttp) cc_final: 0.7554 (mmtt) REVERT: B 45 MET cc_start: 0.8490 (mtp) cc_final: 0.7674 (mtp) REVERT: B 46 ARG cc_start: 0.6950 (tpt-90) cc_final: 0.6508 (mmm-85) REVERT: B 82 TRP cc_start: 0.8696 (m100) cc_final: 0.8286 (m100) REVERT: B 170 ASP cc_start: 0.6806 (t0) cc_final: 0.6461 (t0) REVERT: B 189 SER cc_start: 0.9077 (t) cc_final: 0.8722 (p) REVERT: B 191 SER cc_start: 0.8294 (t) cc_final: 0.8063 (t) REVERT: B 217 MET cc_start: 0.7913 (ptp) cc_final: 0.7647 (tpt) REVERT: B 270 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8509 (pp) REVERT: G 14 LYS cc_start: 0.7731 (mmmt) cc_final: 0.7332 (tttp) outliers start: 27 outliers final: 21 residues processed: 146 average time/residue: 0.1995 time to fit residues: 40.9790 Evaluate side-chains 141 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 73 optimal weight: 0.0040 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9240 Z= 0.160 Angle : 0.505 6.745 12524 Z= 0.270 Chirality : 0.040 0.153 1376 Planarity : 0.004 0.055 1597 Dihedral : 4.647 36.847 1233 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 12.26 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1105 helix: 3.02 (0.24), residues: 448 sheet: 0.38 (0.36), residues: 198 loop : -1.27 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 110 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE R 385 TYR 0.016 0.001 TYR R 242 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4279 (OUTLIER) cc_final: 0.3693 (m-30) REVERT: R 120 TRP cc_start: 0.5542 (t60) cc_final: 0.5284 (t60) REVERT: R 123 LEU cc_start: 0.5110 (OUTLIER) cc_final: 0.4727 (tp) REVERT: R 127 GLU cc_start: 0.6439 (tp30) cc_final: 0.6093 (mt-10) REVERT: R 139 GLU cc_start: 0.7282 (tt0) cc_final: 0.6382 (pm20) REVERT: R 247 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7793 (tp30) REVERT: R 267 ARG cc_start: 0.6455 (mmm-85) cc_final: 0.6229 (mtp180) REVERT: R 305 TYR cc_start: 0.7778 (m-10) cc_final: 0.7487 (m-10) REVERT: R 354 LEU cc_start: 0.8218 (mt) cc_final: 0.7937 (tt) REVERT: R 404 PHE cc_start: 0.4365 (t80) cc_final: 0.3464 (m-80) REVERT: A 27 GLU cc_start: 0.7471 (pp20) cc_final: 0.7188 (pp20) REVERT: A 286 SER cc_start: 0.9141 (m) cc_final: 0.8699 (p) REVERT: A 386 MET cc_start: 0.8918 (ttp) cc_final: 0.8696 (tmm) REVERT: A 389 ARG cc_start: 0.7901 (mmt90) cc_final: 0.7668 (mmt90) REVERT: B 23 LYS cc_start: 0.8420 (tttp) cc_final: 0.7581 (mmtt) REVERT: B 45 MET cc_start: 0.8462 (mtp) cc_final: 0.7695 (mtp) REVERT: B 46 ARG cc_start: 0.6954 (tpt-90) cc_final: 0.6655 (mtp-110) REVERT: B 82 TRP cc_start: 0.8715 (m100) cc_final: 0.8287 (m100) REVERT: B 170 ASP cc_start: 0.6818 (t0) cc_final: 0.6494 (t0) REVERT: B 189 SER cc_start: 0.9093 (t) cc_final: 0.8740 (p) REVERT: B 191 SER cc_start: 0.8331 (t) cc_final: 0.8101 (t) REVERT: B 217 MET cc_start: 0.7938 (ptp) cc_final: 0.7613 (tpt) REVERT: B 270 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8478 (pp) REVERT: G 14 LYS cc_start: 0.7692 (mmmt) cc_final: 0.7318 (tttp) REVERT: N 39 GLN cc_start: 0.7993 (tt0) cc_final: 0.7542 (tp-100) REVERT: N 60 TYR cc_start: 0.8458 (m-80) cc_final: 0.8178 (m-80) outliers start: 31 outliers final: 24 residues processed: 148 average time/residue: 0.1953 time to fit residues: 40.5306 Evaluate side-chains 145 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9240 Z= 0.138 Angle : 0.491 6.863 12524 Z= 0.262 Chirality : 0.039 0.150 1376 Planarity : 0.004 0.053 1597 Dihedral : 4.517 35.601 1233 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.99 % Allowed : 13.59 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1105 helix: 2.93 (0.24), residues: 448 sheet: 0.40 (0.37), residues: 198 loop : -1.24 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 243 HIS 0.003 0.001 HIS R 99 PHE 0.019 0.001 PHE R 367 TYR 0.014 0.001 TYR R 69 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4326 (OUTLIER) cc_final: 0.3891 (m-30) REVERT: R 123 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4684 (tp) REVERT: R 127 GLU cc_start: 0.6381 (tp30) cc_final: 0.6047 (mt-10) REVERT: R 139 GLU cc_start: 0.7270 (tt0) cc_final: 0.6389 (pm20) REVERT: R 220 TYR cc_start: 0.7910 (t80) cc_final: 0.7620 (t80) REVERT: R 247 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: R 267 ARG cc_start: 0.6428 (mmm-85) cc_final: 0.6193 (mtp180) REVERT: R 305 TYR cc_start: 0.7770 (m-10) cc_final: 0.7499 (m-10) REVERT: R 354 LEU cc_start: 0.8243 (mt) cc_final: 0.7961 (tt) REVERT: R 404 PHE cc_start: 0.4240 (t80) cc_final: 0.3489 (m-80) REVERT: A 27 GLU cc_start: 0.7544 (pp20) cc_final: 0.7223 (pp20) REVERT: A 286 SER cc_start: 0.9123 (m) cc_final: 0.8672 (p) REVERT: A 386 MET cc_start: 0.8917 (ttp) cc_final: 0.8694 (tmm) REVERT: A 389 ARG cc_start: 0.7867 (mmt90) cc_final: 0.7630 (mmt90) REVERT: B 23 LYS cc_start: 0.8445 (tttp) cc_final: 0.7558 (mmtt) REVERT: B 42 ARG cc_start: 0.6282 (ttp-110) cc_final: 0.5845 (ttt180) REVERT: B 46 ARG cc_start: 0.6974 (tpt-90) cc_final: 0.6725 (mtp-110) REVERT: B 82 TRP cc_start: 0.8703 (m100) cc_final: 0.8451 (m100) REVERT: B 170 ASP cc_start: 0.6730 (t0) cc_final: 0.6517 (t0) REVERT: B 189 SER cc_start: 0.9084 (t) cc_final: 0.8741 (p) REVERT: B 191 SER cc_start: 0.8342 (t) cc_final: 0.8113 (t) REVERT: B 217 MET cc_start: 0.7970 (ptp) cc_final: 0.7629 (tpt) REVERT: B 270 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8494 (pp) REVERT: G 14 LYS cc_start: 0.7687 (mmmt) cc_final: 0.7317 (tttp) REVERT: N 39 GLN cc_start: 0.8005 (tt0) cc_final: 0.7559 (tp-100) REVERT: N 60 TYR cc_start: 0.8405 (m-80) cc_final: 0.8089 (m-80) outliers start: 29 outliers final: 22 residues processed: 150 average time/residue: 0.2008 time to fit residues: 41.8906 Evaluate side-chains 148 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN N 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9240 Z= 0.331 Angle : 0.619 9.756 12524 Z= 0.329 Chirality : 0.043 0.169 1376 Planarity : 0.004 0.053 1597 Dihedral : 4.957 36.915 1233 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.19 % Allowed : 14.11 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1105 helix: 2.93 (0.24), residues: 439 sheet: 0.06 (0.35), residues: 218 loop : -1.38 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 110 HIS 0.010 0.001 HIS B 54 PHE 0.026 0.002 PHE N 29 TYR 0.020 0.002 TYR R 402 ARG 0.004 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: R 139 GLU cc_start: 0.7344 (tt0) cc_final: 0.6454 (pm20) REVERT: R 247 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: R 267 ARG cc_start: 0.6456 (mmm-85) cc_final: 0.6191 (mtp180) REVERT: R 305 TYR cc_start: 0.7804 (m-10) cc_final: 0.7577 (m-10) REVERT: R 354 LEU cc_start: 0.8282 (mt) cc_final: 0.7994 (tt) REVERT: R 404 PHE cc_start: 0.4168 (t80) cc_final: 0.3467 (m-80) REVERT: P 13 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8468 (mmmm) REVERT: A 27 GLU cc_start: 0.7666 (pp20) cc_final: 0.7328 (pp20) REVERT: A 286 SER cc_start: 0.9159 (m) cc_final: 0.8631 (p) REVERT: B 23 LYS cc_start: 0.8596 (tttp) cc_final: 0.7612 (mmtt) REVERT: B 46 ARG cc_start: 0.7004 (tpt-90) cc_final: 0.6529 (mmm-85) REVERT: B 59 TYR cc_start: 0.8490 (t80) cc_final: 0.8211 (t80) REVERT: B 82 TRP cc_start: 0.8802 (m100) cc_final: 0.8502 (m100) REVERT: B 170 ASP cc_start: 0.7059 (t0) cc_final: 0.6849 (t0) REVERT: B 189 SER cc_start: 0.9207 (t) cc_final: 0.8817 (p) REVERT: B 191 SER cc_start: 0.8487 (t) cc_final: 0.7978 (p) REVERT: B 217 MET cc_start: 0.7922 (ptp) cc_final: 0.7653 (tpt) REVERT: B 270 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8476 (pp) REVERT: G 14 LYS cc_start: 0.7666 (mmmt) cc_final: 0.7280 (tttp) outliers start: 31 outliers final: 26 residues processed: 134 average time/residue: 0.1916 time to fit residues: 36.8677 Evaluate side-chains 131 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 234 GLN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9240 Z= 0.186 Angle : 0.548 7.453 12524 Z= 0.290 Chirality : 0.040 0.166 1376 Planarity : 0.004 0.052 1597 Dihedral : 4.738 36.062 1233 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.19 % Allowed : 14.42 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1105 helix: 2.97 (0.24), residues: 442 sheet: 0.04 (0.35), residues: 213 loop : -1.35 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 417 HIS 0.008 0.001 HIS B 54 PHE 0.022 0.002 PHE R 385 TYR 0.013 0.001 TYR R 69 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 1.058 Fit side-chains REVERT: R 67 ASP cc_start: 0.4487 (OUTLIER) cc_final: 0.3875 (m-30) REVERT: R 139 GLU cc_start: 0.7299 (tt0) cc_final: 0.6431 (pm20) REVERT: R 247 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7796 (tp30) REVERT: R 267 ARG cc_start: 0.6406 (mmm-85) cc_final: 0.6146 (mtp180) REVERT: R 269 TYR cc_start: 0.8438 (m-80) cc_final: 0.8208 (m-80) REVERT: R 354 LEU cc_start: 0.8369 (mt) cc_final: 0.8062 (tt) REVERT: R 404 PHE cc_start: 0.4123 (t80) cc_final: 0.3458 (m-80) REVERT: P 13 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8469 (mmmm) REVERT: A 27 GLU cc_start: 0.7664 (pp20) cc_final: 0.7319 (pp20) REVERT: A 286 SER cc_start: 0.9140 (m) cc_final: 0.8632 (p) REVERT: B 23 LYS cc_start: 0.8530 (tttp) cc_final: 0.7584 (mmtt) REVERT: B 82 TRP cc_start: 0.8769 (m100) cc_final: 0.8462 (m100) REVERT: B 189 SER cc_start: 0.9150 (t) cc_final: 0.8782 (p) REVERT: B 191 SER cc_start: 0.8413 (t) cc_final: 0.8169 (t) REVERT: B 217 MET cc_start: 0.7947 (ptp) cc_final: 0.7662 (tpt) REVERT: B 270 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8477 (pp) REVERT: G 14 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7282 (tttp) REVERT: N 60 TYR cc_start: 0.8460 (m-80) cc_final: 0.8028 (m-80) outliers start: 31 outliers final: 25 residues processed: 136 average time/residue: 0.1989 time to fit residues: 38.3606 Evaluate side-chains 134 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9240 Z= 0.195 Angle : 0.561 7.755 12524 Z= 0.296 Chirality : 0.040 0.154 1376 Planarity : 0.004 0.052 1597 Dihedral : 4.700 35.219 1233 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.19 % Allowed : 14.21 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1105 helix: 2.94 (0.24), residues: 442 sheet: 0.01 (0.35), residues: 213 loop : -1.30 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 110 HIS 0.007 0.001 HIS B 54 PHE 0.022 0.002 PHE R 385 TYR 0.014 0.001 TYR R 69 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 1.107 Fit side-chains REVERT: R 67 ASP cc_start: 0.4374 (OUTLIER) cc_final: 0.3800 (m-30) REVERT: R 120 TRP cc_start: 0.5457 (t60) cc_final: 0.4956 (t60) REVERT: R 127 GLU cc_start: 0.6474 (tp30) cc_final: 0.5868 (pt0) REVERT: R 139 GLU cc_start: 0.7261 (tt0) cc_final: 0.6437 (pm20) REVERT: R 247 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7798 (tp30) REVERT: R 267 ARG cc_start: 0.6469 (mmm-85) cc_final: 0.6203 (mtp180) REVERT: R 269 TYR cc_start: 0.8432 (m-80) cc_final: 0.8178 (m-80) REVERT: R 354 LEU cc_start: 0.8378 (mt) cc_final: 0.8067 (tt) REVERT: R 404 PHE cc_start: 0.4216 (t80) cc_final: 0.3429 (m-80) REVERT: P 10 ASP cc_start: 0.8046 (t0) cc_final: 0.7836 (t0) REVERT: A 27 GLU cc_start: 0.7698 (pp20) cc_final: 0.7339 (pp20) REVERT: A 286 SER cc_start: 0.9138 (m) cc_final: 0.8629 (p) REVERT: B 23 LYS cc_start: 0.8536 (tttp) cc_final: 0.7582 (mmtt) REVERT: B 45 MET cc_start: 0.7230 (mmp) cc_final: 0.6951 (mmp) REVERT: B 46 ARG cc_start: 0.6921 (tpp80) cc_final: 0.6561 (mpt180) REVERT: B 82 TRP cc_start: 0.8779 (m100) cc_final: 0.8475 (m100) REVERT: B 111 TYR cc_start: 0.8765 (m-80) cc_final: 0.8551 (m-10) REVERT: B 189 SER cc_start: 0.9154 (t) cc_final: 0.8790 (p) REVERT: B 191 SER cc_start: 0.8378 (t) cc_final: 0.8143 (t) REVERT: B 217 MET cc_start: 0.7907 (ptp) cc_final: 0.7636 (tpt) REVERT: B 270 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8479 (pp) REVERT: G 14 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7280 (tttp) outliers start: 31 outliers final: 25 residues processed: 133 average time/residue: 0.1939 time to fit residues: 36.6199 Evaluate side-chains 134 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9240 Z= 0.210 Angle : 0.580 8.147 12524 Z= 0.303 Chirality : 0.040 0.156 1376 Planarity : 0.004 0.052 1597 Dihedral : 4.708 35.621 1233 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.99 % Allowed : 14.32 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.26), residues: 1105 helix: 2.98 (0.24), residues: 439 sheet: -0.02 (0.35), residues: 213 loop : -1.37 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 110 HIS 0.007 0.001 HIS B 54 PHE 0.022 0.002 PHE R 385 TYR 0.014 0.002 TYR R 69 ARG 0.003 0.000 ARG B 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: R 67 ASP cc_start: 0.4385 (OUTLIER) cc_final: 0.3798 (m-30) REVERT: R 120 TRP cc_start: 0.5542 (t60) cc_final: 0.5065 (t60) REVERT: R 127 GLU cc_start: 0.6452 (tp30) cc_final: 0.5949 (mt-10) REVERT: R 139 GLU cc_start: 0.7307 (tt0) cc_final: 0.6410 (pm20) REVERT: R 242 TYR cc_start: 0.8187 (m-80) cc_final: 0.7766 (m-80) REVERT: R 247 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7798 (tp30) REVERT: R 267 ARG cc_start: 0.6561 (mmm-85) cc_final: 0.6297 (mtp180) REVERT: R 269 TYR cc_start: 0.8391 (m-80) cc_final: 0.8173 (m-80) REVERT: R 354 LEU cc_start: 0.8352 (mt) cc_final: 0.8044 (tt) REVERT: R 404 PHE cc_start: 0.4292 (t80) cc_final: 0.3479 (m-80) REVERT: P 10 ASP cc_start: 0.8042 (t0) cc_final: 0.7832 (t0) REVERT: A 27 GLU cc_start: 0.7702 (pp20) cc_final: 0.7338 (pp20) REVERT: A 286 SER cc_start: 0.9146 (m) cc_final: 0.8640 (p) REVERT: B 23 LYS cc_start: 0.8587 (tttp) cc_final: 0.7641 (mmtt) REVERT: B 45 MET cc_start: 0.7344 (mmp) cc_final: 0.6945 (mmp) REVERT: B 82 TRP cc_start: 0.8780 (m100) cc_final: 0.8475 (m100) REVERT: B 189 SER cc_start: 0.9166 (t) cc_final: 0.8806 (p) REVERT: B 191 SER cc_start: 0.8389 (t) cc_final: 0.8154 (t) REVERT: B 217 MET cc_start: 0.7908 (ptp) cc_final: 0.7636 (tpt) REVERT: B 270 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8493 (pp) REVERT: G 14 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7273 (tttp) outliers start: 29 outliers final: 24 residues processed: 128 average time/residue: 0.1893 time to fit residues: 34.5059 Evaluate side-chains 132 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 198 ASP Chi-restraints excluded: chain R residue 247 GLU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 4 optimal weight: 0.2980 chunk 63 optimal weight: 0.3980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.114565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.100195 restraints weight = 23502.583| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.79 r_work: 0.3586 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9240 Z= 0.206 Angle : 0.569 7.903 12524 Z= 0.297 Chirality : 0.040 0.153 1376 Planarity : 0.004 0.051 1597 Dihedral : 4.680 35.392 1233 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.99 % Allowed : 14.32 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 2.94 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1105 helix: 2.94 (0.24), residues: 442 sheet: -0.01 (0.35), residues: 213 loop : -1.34 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 110 HIS 0.006 0.001 HIS B 54 PHE 0.023 0.002 PHE R 381 TYR 0.013 0.001 TYR R 69 ARG 0.003 0.000 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1942.45 seconds wall clock time: 35 minutes 39.75 seconds (2139.75 seconds total)