Starting phenix.real_space_refine on Thu Mar 13 05:49:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1f_33562/03_2025/7y1f_33562.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1f_33562/03_2025/7y1f_33562.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/cci-nas-00/data/ceres_data/7y1f_33562/03_2025/7y1f_33562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1f_33562/03_2025/7y1f_33562.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1f_33562/03_2025/7y1f_33562.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1f_33562/03_2025/7y1f_33562.cif" } 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= 0.000 sd= 0.003 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 60 5.16 5 C 5561 2.51 5 N 1480 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2256 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 5.01, per 1000 atoms: 0.58 Number of scatterers: 8691 At special positions: 0 Unit cell: (102.6, 112.32, 135, 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 60 16.00 O 1590 8.00 N 1480 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 233 " - pdb=" SG CYS R 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 35.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.238A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.575A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.208A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.571A pdb=" N SER A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.979A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.971A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 345 Processing helix chain 'R' and resid 159 through 189 Processing helix chain 'R' and resid 194 through 212 removed outlier: 3.768A pdb=" N ILE R 198 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 223 removed outlier: 4.097A pdb=" N VAL R 220 " --> pdb=" O PHE R 216 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 264 removed outlier: 3.568A pdb=" N HIS R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 272 removed outlier: 4.019A pdb=" N LEU R 269 " --> pdb=" O PRO R 265 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP R 270 " --> pdb=" O VAL R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 298 removed outlier: 4.137A pdb=" N VAL R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 337 Processing helix chain 'R' and resid 337 through 357 removed outlier: 4.213A pdb=" N SER R 357 " --> pdb=" O LEU R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 399 removed outlier: 3.782A pdb=" N ASP R 368 " --> pdb=" O SER R 364 " (cutoff:3.500A) Proline residue: R 391 - end of helix Processing helix chain 'R' and resid 409 through 433 removed outlier: 4.344A pdb=" N SER R 413 " --> pdb=" O ALA R 409 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER R 425 " --> pdb=" O GLY R 421 " (cutoff:3.500A) Proline residue: R 429 - end of helix Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.965A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.859A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.615A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.519A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.545A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.392A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226 removed outlier: 5.654A pdb=" N PHE A 223 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 299 through 302 removed outlier: 3.794A pdb=" N GLY R 300 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER R 313 " --> pdb=" O GLY R 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 311 " --> pdb=" O LYS R 302 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.696A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.167A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.470A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.690A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.700A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.777A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.137A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1131 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: 2.68 Time building geometry restraints manager: 2.51 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: 2767 1.34 - 1.47: 2247 1.47 - 1.59: 3770 1.59 - 1.72: 0 1.72 - 1.84: 87 Bond restraints: 8871 Sorted by residual: bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.335 1.247 0.087 3.04e-02 1.08e+03 8.23e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.414 0.099 3.90e-02 6.57e+02 6.49e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.45e+00 bond pdb=" CG1 ILE B 338 " pdb=" CD1 ILE B 338 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.29e+00 bond pdb=" CB VAL B 112 " pdb=" CG1 VAL B 112 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 8866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 11807 3.38 - 6.75: 200 6.75 - 10.13: 26 10.13 - 13.50: 1 13.50 - 16.88: 1 Bond angle restraints: 12035 Sorted by residual: angle pdb=" C GLU R 305 " pdb=" N ASP R 306 " pdb=" CA ASP R 306 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" CA LEU A 353 " pdb=" CB LEU A 353 " pdb=" CG LEU A 353 " ideal model delta sigma weight residual 116.30 133.18 -16.88 3.50e+00 8.16e-02 2.33e+01 angle pdb=" C ALA E 209 " pdb=" N GLU E 210 " pdb=" CA GLU E 210 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ASP B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta sigma weight residual 122.74 128.70 -5.96 1.44e+00 4.82e-01 1.71e+01 angle pdb=" C ASP B 246 " pdb=" N ASP B 247 " pdb=" CA ASP B 247 " ideal model delta sigma weight residual 120.60 127.21 -6.61 1.60e+00 3.91e-01 1.71e+01 ... (remaining 12030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4701 17.11 - 34.23: 435 34.23 - 51.34: 93 51.34 - 68.45: 8 68.45 - 85.57: 10 Dihedral angle restraints: 5247 sinusoidal: 1964 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 170.63 -77.63 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CA LYS A 10 " pdb=" C LYS A 10 " pdb=" N ALA A 11 " pdb=" CA ALA A 11 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA LYS A 349 " pdb=" C LYS A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1214 0.084 - 0.169: 164 0.169 - 0.253: 16 0.253 - 0.338: 2 0.338 - 0.422: 2 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB ILE B 338 " pdb=" CA ILE B 338 " pdb=" CG1 ILE B 338 " pdb=" CG2 ILE B 338 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1395 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.032 2.00e-02 2.50e+03 2.61e-02 1.70e+01 pdb=" CG TRP B 332 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 214 " 0.066 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO R 215 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.021 2.00e-02 2.50e+03 1.90e-02 7.22e+00 pdb=" CG TYR B 105 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.001 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1297 2.75 - 3.29: 8569 3.29 - 3.83: 14672 3.83 - 4.36: 17392 4.36 - 4.90: 30149 Nonbonded interactions: 72079 Sorted by model distance: nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.215 3.040 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.234 3.040 nonbonded pdb=" O ALA R 419 " pdb=" OG1 THR R 423 " model vdw 2.241 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.242 3.040 nonbonded pdb=" O VAL R 386 " pdb=" OG1 THR R 390 " model vdw 2.250 3.040 ... (remaining 72074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.099 8871 Z= 0.463 Angle : 1.118 16.879 12035 Z= 0.604 Chirality : 0.060 0.422 1398 Planarity : 0.007 0.098 1505 Dihedral : 13.790 85.567 3117 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % 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: -2.25 (0.23), residues: 1113 helix: -1.02 (0.24), residues: 357 sheet: -1.36 (0.33), residues: 251 loop : -1.81 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP B 332 HIS 0.013 0.003 HIS B 183 PHE 0.034 0.003 PHE A 323 TYR 0.047 0.003 TYR B 105 ARG 0.028 0.002 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.018 Fit side-chains REVERT: A 303 ILE cc_start: 0.7538 (mt) cc_final: 0.7302 (mm) REVERT: A 333 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7379 (tp40) REVERT: A 337 ASP cc_start: 0.7943 (m-30) cc_final: 0.7657 (m-30) REVERT: R 214 MET cc_start: 0.6920 (ttm) cc_final: 0.6566 (ttp) REVERT: R 221 TYR cc_start: 0.7337 (t80) cc_final: 0.6873 (t80) REVERT: R 222 LEU cc_start: 0.6161 (mm) cc_final: 0.5681 (mm) REVERT: B 43 ILE cc_start: 0.8389 (mt) cc_final: 0.8066 (mt) REVERT: E 223 TYR cc_start: 0.7885 (m-80) cc_final: 0.7077 (m-80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2075 time to fit residues: 65.9053 Evaluate side-chains 197 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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: 0.0670 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.0050 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 322 HIS ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 266 HIS E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.207638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.165628 restraints weight = 10264.232| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.43 r_work: 0.3816 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8871 Z= 0.184 Angle : 0.656 9.753 12035 Z= 0.345 Chirality : 0.044 0.233 1398 Planarity : 0.005 0.065 1505 Dihedral : 5.589 24.183 1224 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.73 % Allowed : 8.97 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1113 helix: 0.61 (0.26), residues: 334 sheet: -1.10 (0.33), residues: 250 loop : -1.46 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 332 HIS 0.004 0.001 HIS A 188 PHE 0.032 0.002 PHE R 439 TYR 0.019 0.001 TYR R 242 ARG 0.006 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 258 TRP cc_start: 0.5380 (m100) cc_final: 0.2973 (p-90) REVERT: A 333 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7375 (tp40) REVERT: A 337 ASP cc_start: 0.7957 (m-30) cc_final: 0.7751 (m-30) REVERT: R 187 ILE cc_start: 0.7025 (mm) cc_final: 0.6660 (mt) REVERT: R 214 MET cc_start: 0.6886 (ttm) cc_final: 0.6537 (ttm) REVERT: R 223 MET cc_start: 0.7309 (tmm) cc_final: 0.7094 (ppp) REVERT: R 315 GLN cc_start: 0.5657 (mp10) cc_final: 0.5023 (mp10) REVERT: R 351 MET cc_start: 0.8043 (ttt) cc_final: 0.7810 (ttt) REVERT: B 79 LEU cc_start: 0.8379 (mt) cc_final: 0.8058 (mt) REVERT: C 32 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8107 (mmtm) REVERT: E 47 TRP cc_start: 0.7002 (t60) cc_final: 0.6548 (t60) REVERT: E 206 ARG cc_start: 0.8045 (tpp-160) cc_final: 0.7744 (tpp-160) outliers start: 16 outliers final: 13 residues processed: 225 average time/residue: 0.2575 time to fit residues: 78.3957 Evaluate side-chains 204 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 266 HIS ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.197711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154368 restraints weight = 10643.906| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.44 r_work: 0.3667 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8871 Z= 0.388 Angle : 0.746 8.670 12035 Z= 0.392 Chirality : 0.047 0.374 1398 Planarity : 0.005 0.056 1505 Dihedral : 5.855 28.998 1224 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.68 % Allowed : 11.89 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1113 helix: 0.58 (0.26), residues: 345 sheet: -1.13 (0.32), residues: 257 loop : -1.45 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 332 HIS 0.007 0.002 HIS A 244 PHE 0.021 0.002 PHE R 439 TYR 0.024 0.002 TYR B 105 ARG 0.008 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7830 (mmp) cc_final: 0.6909 (mmp) REVERT: A 333 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7750 (tp40) REVERT: A 337 ASP cc_start: 0.8058 (m-30) cc_final: 0.7712 (m-30) REVERT: R 187 ILE cc_start: 0.6977 (mm) cc_final: 0.6626 (mt) REVERT: R 214 MET cc_start: 0.7261 (ttm) cc_final: 0.6969 (ttm) REVERT: R 223 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6986 (ppp) REVERT: R 354 ARG cc_start: 0.7755 (tpp80) cc_final: 0.6166 (tpt90) REVERT: B 256 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7472 (ttm110) REVERT: C 32 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8107 (mmtm) REVERT: E 47 TRP cc_start: 0.7233 (t60) cc_final: 0.6966 (t60) REVERT: E 93 MET cc_start: 0.6354 (tmm) cc_final: 0.6109 (ptm) REVERT: E 160 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7527 (m) outliers start: 34 outliers final: 26 residues processed: 229 average time/residue: 0.2416 time to fit residues: 75.9779 Evaluate side-chains 218 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 386 VAL Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 86 optimal weight: 0.0670 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.205796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.162870 restraints weight = 10438.724| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.44 r_work: 0.3755 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8871 Z= 0.204 Angle : 0.651 8.981 12035 Z= 0.338 Chirality : 0.044 0.225 1398 Planarity : 0.004 0.049 1505 Dihedral : 5.388 24.147 1224 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.49 % Allowed : 16.11 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1113 helix: 1.03 (0.26), residues: 339 sheet: -0.90 (0.33), residues: 247 loop : -1.30 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 332 HIS 0.003 0.001 HIS A 213 PHE 0.036 0.002 PHE A 323 TYR 0.016 0.001 TYR R 242 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 1.121 Fit side-chains REVERT: A 247 MET cc_start: 0.7814 (mmp) cc_final: 0.7150 (mmp) REVERT: A 333 GLN cc_start: 0.7991 (mm110) cc_final: 0.7571 (tp40) REVERT: A 337 ASP cc_start: 0.8025 (m-30) cc_final: 0.7524 (m-30) REVERT: R 187 ILE cc_start: 0.6854 (mm) cc_final: 0.6482 (mt) REVERT: R 214 MET cc_start: 0.7337 (ttm) cc_final: 0.6939 (ttm) REVERT: R 223 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6829 (ppp) REVERT: R 354 ARG cc_start: 0.7751 (tpp80) cc_final: 0.6196 (tpt90) REVERT: B 82 TRP cc_start: 0.7111 (m100) cc_final: 0.6565 (m100) REVERT: B 226 GLU cc_start: 0.7884 (mp0) cc_final: 0.7643 (mm-30) REVERT: B 256 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7531 (ttm110) REVERT: C 21 MET cc_start: 0.4053 (tmm) cc_final: 0.3707 (tmm) REVERT: C 32 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8099 (mmtm) REVERT: E 47 TRP cc_start: 0.7039 (t60) cc_final: 0.6545 (t60) REVERT: E 93 MET cc_start: 0.6475 (OUTLIER) cc_final: 0.6185 (ptm) REVERT: E 160 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7432 (m) outliers start: 23 outliers final: 17 residues processed: 225 average time/residue: 0.2672 time to fit residues: 82.0170 Evaluate side-chains 217 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS E 219 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.201935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158985 restraints weight = 10428.227| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.42 r_work: 0.3712 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8871 Z= 0.267 Angle : 0.668 8.754 12035 Z= 0.348 Chirality : 0.045 0.264 1398 Planarity : 0.004 0.047 1505 Dihedral : 5.426 27.062 1224 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.89 % Allowed : 16.76 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.65 (0.25), residues: 1113 helix: 1.18 (0.26), residues: 339 sheet: -1.03 (0.33), residues: 253 loop : -1.17 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 99 HIS 0.004 0.001 HIS A 213 PHE 0.033 0.002 PHE R 439 TYR 0.014 0.002 TYR R 242 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.875 Fit side-chains REVERT: A 247 MET cc_start: 0.7762 (mmp) cc_final: 0.7375 (mmp) REVERT: A 333 GLN cc_start: 0.8053 (mm110) cc_final: 0.7613 (tp40) REVERT: A 337 ASP cc_start: 0.7929 (m-30) cc_final: 0.7443 (m-30) REVERT: A 341 ASP cc_start: 0.7969 (m-30) cc_final: 0.7693 (m-30) REVERT: R 187 ILE cc_start: 0.6847 (mm) cc_final: 0.6466 (mt) REVERT: R 198 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.6637 (pt) REVERT: R 214 MET cc_start: 0.7424 (ttm) cc_final: 0.7080 (ttm) REVERT: R 223 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6958 (ppp) REVERT: R 354 ARG cc_start: 0.7734 (tpp80) cc_final: 0.6183 (tpt90) REVERT: B 45 MET cc_start: 0.8464 (mpp) cc_final: 0.8256 (mpp) REVERT: B 183 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7046 (m170) REVERT: B 226 GLU cc_start: 0.7903 (mp0) cc_final: 0.7640 (mm-30) REVERT: B 256 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7390 (ttm110) REVERT: E 47 TRP cc_start: 0.7054 (t60) cc_final: 0.6669 (t60) REVERT: E 93 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6226 (ptm) REVERT: E 160 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7461 (m) outliers start: 36 outliers final: 26 residues processed: 226 average time/residue: 0.2095 time to fit residues: 64.5782 Evaluate side-chains 227 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.205071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.162970 restraints weight = 10402.518| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.42 r_work: 0.3760 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8871 Z= 0.219 Angle : 0.646 8.532 12035 Z= 0.337 Chirality : 0.044 0.249 1398 Planarity : 0.004 0.044 1505 Dihedral : 5.244 25.221 1224 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.35 % Allowed : 18.27 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1113 helix: 1.26 (0.26), residues: 345 sheet: -0.96 (0.33), residues: 256 loop : -1.16 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 99 HIS 0.003 0.001 HIS A 213 PHE 0.033 0.002 PHE R 439 TYR 0.017 0.001 TYR A 296 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.041 Fit side-chains REVERT: A 334 PHE cc_start: 0.7925 (t80) cc_final: 0.7712 (t80) REVERT: A 337 ASP cc_start: 0.7909 (m-30) cc_final: 0.7311 (m-30) REVERT: A 341 ASP cc_start: 0.8080 (m-30) cc_final: 0.7778 (m-30) REVERT: R 187 ILE cc_start: 0.6782 (mm) cc_final: 0.6486 (mp) REVERT: R 214 MET cc_start: 0.7482 (ttm) cc_final: 0.7136 (ttm) REVERT: R 223 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6964 (ppp) REVERT: R 354 ARG cc_start: 0.7749 (tpp80) cc_final: 0.6252 (tpt90) REVERT: B 45 MET cc_start: 0.8430 (mpp) cc_final: 0.8217 (mpp) REVERT: B 82 TRP cc_start: 0.7216 (m100) cc_final: 0.6672 (m100) REVERT: B 183 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7043 (m170) REVERT: B 226 GLU cc_start: 0.7921 (mp0) cc_final: 0.7620 (mm-30) REVERT: B 256 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7401 (ttm110) REVERT: E 47 TRP cc_start: 0.6891 (t60) cc_final: 0.6399 (t60) REVERT: E 93 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6292 (ptm) REVERT: E 160 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7423 (m) outliers start: 31 outliers final: 24 residues processed: 226 average time/residue: 0.2138 time to fit residues: 66.0633 Evaluate side-chains 232 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 67 optimal weight: 0.0970 chunk 88 optimal weight: 0.0970 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.208231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.165546 restraints weight = 10563.752| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.49 r_work: 0.3842 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8871 Z= 0.184 Angle : 0.637 8.540 12035 Z= 0.328 Chirality : 0.043 0.221 1398 Planarity : 0.004 0.048 1505 Dihedral : 5.015 22.901 1224 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.78 % Allowed : 19.03 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.37 (0.25), residues: 1113 helix: 1.46 (0.27), residues: 344 sheet: -0.79 (0.33), residues: 256 loop : -1.11 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS R 393 PHE 0.034 0.002 PHE R 439 TYR 0.022 0.001 TYR A 296 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.954 Fit side-chains REVERT: A 247 MET cc_start: 0.7665 (mmp) cc_final: 0.7122 (mmp) REVERT: A 334 PHE cc_start: 0.7827 (t80) cc_final: 0.7616 (t80) REVERT: A 337 ASP cc_start: 0.7880 (m-30) cc_final: 0.7277 (m-30) REVERT: A 341 ASP cc_start: 0.8101 (m-30) cc_final: 0.7783 (m-30) REVERT: R 187 ILE cc_start: 0.6799 (mm) cc_final: 0.6510 (mp) REVERT: R 214 MET cc_start: 0.7458 (ttm) cc_final: 0.7228 (ttm) REVERT: R 223 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6878 (tmm) REVERT: R 354 ARG cc_start: 0.7778 (tpp80) cc_final: 0.6329 (tpt90) REVERT: B 82 TRP cc_start: 0.7145 (m100) cc_final: 0.6608 (m100) REVERT: B 183 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.7079 (m170) REVERT: B 226 GLU cc_start: 0.7876 (mp0) cc_final: 0.7645 (mm-30) REVERT: B 256 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7434 (ttm110) REVERT: C 21 MET cc_start: 0.3910 (tmm) cc_final: 0.3216 (tmm) REVERT: E 47 TRP cc_start: 0.6777 (t60) cc_final: 0.6233 (t60) REVERT: E 160 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7316 (m) outliers start: 35 outliers final: 25 residues processed: 234 average time/residue: 0.2079 time to fit residues: 66.2012 Evaluate side-chains 232 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 86 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.207876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.165343 restraints weight = 10496.240| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.45 r_work: 0.3804 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8871 Z= 0.191 Angle : 0.644 9.454 12035 Z= 0.329 Chirality : 0.043 0.229 1398 Planarity : 0.004 0.044 1505 Dihedral : 4.963 23.486 1224 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.57 % Allowed : 20.00 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.24 (0.25), residues: 1113 helix: 1.63 (0.27), residues: 343 sheet: -0.65 (0.34), residues: 243 loop : -1.12 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 332 HIS 0.003 0.001 HIS R 393 PHE 0.034 0.002 PHE R 439 TYR 0.024 0.001 TYR A 296 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.999 Fit side-chains REVERT: A 247 MET cc_start: 0.7667 (mmp) cc_final: 0.7087 (mmp) REVERT: A 333 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7846 (tp40) REVERT: A 334 PHE cc_start: 0.7889 (t80) cc_final: 0.7681 (t80) REVERT: A 337 ASP cc_start: 0.7870 (m-30) cc_final: 0.7301 (m-30) REVERT: A 341 ASP cc_start: 0.8112 (m-30) cc_final: 0.7792 (m-30) REVERT: R 214 MET cc_start: 0.7528 (ttm) cc_final: 0.7219 (ttm) REVERT: R 223 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.7042 (tmm) REVERT: R 354 ARG cc_start: 0.7740 (tpp80) cc_final: 0.6245 (tpt90) REVERT: R 366 GLU cc_start: 0.6038 (mm-30) cc_final: 0.5713 (mp0) REVERT: B 45 MET cc_start: 0.8390 (mpp) cc_final: 0.8111 (mpp) REVERT: B 82 TRP cc_start: 0.7189 (m100) cc_final: 0.6649 (m100) REVERT: B 219 ARG cc_start: 0.7901 (ttt90) cc_final: 0.7680 (ttt90) REVERT: B 226 GLU cc_start: 0.7894 (mp0) cc_final: 0.7641 (mm-30) REVERT: B 256 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7463 (ttm110) REVERT: C 21 MET cc_start: 0.4298 (tmm) cc_final: 0.3576 (tmm) REVERT: C 32 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8243 (tppt) REVERT: E 47 TRP cc_start: 0.6863 (t60) cc_final: 0.6437 (t60) REVERT: E 148 ARG cc_start: 0.6695 (ttm-80) cc_final: 0.6434 (ttm-80) REVERT: E 160 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.7286 (m) outliers start: 33 outliers final: 26 residues processed: 224 average time/residue: 0.2192 time to fit residues: 67.3091 Evaluate side-chains 229 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 223 MET Chi-restraints excluded: chain R residue 312 CYS Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 76 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.203156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160027 restraints weight = 10466.460| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.43 r_work: 0.3746 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8871 Z= 0.236 Angle : 0.661 9.162 12035 Z= 0.340 Chirality : 0.044 0.269 1398 Planarity : 0.004 0.043 1505 Dihedral : 5.085 25.643 1224 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.46 % Allowed : 20.32 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.27 (0.25), residues: 1113 helix: 1.63 (0.27), residues: 343 sheet: -0.79 (0.33), residues: 256 loop : -1.07 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 99 HIS 0.003 0.001 HIS A 213 PHE 0.035 0.002 PHE R 439 TYR 0.023 0.002 TYR A 296 ARG 0.009 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.889 Fit side-chains REVERT: A 247 MET cc_start: 0.7656 (mmp) cc_final: 0.7115 (mmp) REVERT: A 333 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7775 (tp40) REVERT: A 337 ASP cc_start: 0.7899 (m-30) cc_final: 0.7263 (m-30) REVERT: A 341 ASP cc_start: 0.8025 (m-30) cc_final: 0.7678 (m-30) REVERT: R 214 MET cc_start: 0.7561 (ttm) cc_final: 0.7288 (ttm) REVERT: R 354 ARG cc_start: 0.7731 (tpp80) cc_final: 0.6194 (tpt90) REVERT: B 45 MET cc_start: 0.8496 (mpp) cc_final: 0.8222 (mpp) REVERT: B 82 TRP cc_start: 0.7277 (m100) cc_final: 0.6704 (m100) REVERT: B 219 ARG cc_start: 0.8020 (ttt90) cc_final: 0.7794 (ttt90) REVERT: B 226 GLU cc_start: 0.7975 (mp0) cc_final: 0.7691 (mm-30) REVERT: B 256 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7380 (ttm110) REVERT: C 21 MET cc_start: 0.3982 (tmm) cc_final: 0.3298 (tmm) REVERT: C 32 LYS cc_start: 0.8536 (ttmm) cc_final: 0.8286 (tppt) REVERT: E 47 TRP cc_start: 0.6972 (t60) cc_final: 0.6562 (t60) REVERT: E 93 MET cc_start: 0.7084 (ptm) cc_final: 0.6582 (ttp) outliers start: 32 outliers final: 28 residues processed: 220 average time/residue: 0.2235 time to fit residues: 68.1367 Evaluate side-chains 231 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 312 CYS Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 21 optimal weight: 0.0000 chunk 89 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 86 optimal weight: 0.0050 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.210991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.168607 restraints weight = 10372.356| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.46 r_work: 0.3818 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8871 Z= 0.171 Angle : 0.636 8.798 12035 Z= 0.327 Chirality : 0.043 0.206 1398 Planarity : 0.004 0.042 1505 Dihedral : 4.831 23.930 1224 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.92 % Allowed : 21.08 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1113 helix: 1.78 (0.27), residues: 341 sheet: -0.75 (0.33), residues: 247 loop : -1.11 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.003 0.001 HIS A 188 PHE 0.025 0.001 PHE A 334 TYR 0.024 0.001 TYR A 296 ARG 0.009 0.001 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.910 Fit side-chains REVERT: A 333 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7982 (tp40) REVERT: A 337 ASP cc_start: 0.7828 (m-30) cc_final: 0.7269 (m-30) REVERT: A 341 ASP cc_start: 0.8094 (m-30) cc_final: 0.7776 (m-30) REVERT: R 214 MET cc_start: 0.7471 (ttm) cc_final: 0.7253 (ttm) REVERT: R 253 MET cc_start: 0.7722 (tpp) cc_final: 0.7428 (tpp) REVERT: B 49 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7855 (mtm-85) REVERT: B 79 LEU cc_start: 0.8319 (mt) cc_final: 0.8050 (mt) REVERT: B 82 TRP cc_start: 0.7126 (m100) cc_final: 0.6586 (m100) REVERT: B 219 ARG cc_start: 0.7790 (ttt90) cc_final: 0.7538 (ttt90) REVERT: B 256 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7370 (ttm110) REVERT: B 298 ASP cc_start: 0.7999 (t70) cc_final: 0.7687 (t0) REVERT: C 21 MET cc_start: 0.4305 (tmm) cc_final: 0.3678 (tmm) REVERT: C 32 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8267 (tppt) REVERT: E 47 TRP cc_start: 0.6715 (t60) cc_final: 0.6169 (t60) REVERT: E 93 MET cc_start: 0.7082 (ptm) cc_final: 0.6599 (ttp) REVERT: E 148 ARG cc_start: 0.6762 (ttm-80) cc_final: 0.6473 (ttm-80) REVERT: E 216 TYR cc_start: 0.7818 (m-80) cc_final: 0.7616 (m-80) outliers start: 27 outliers final: 24 residues processed: 219 average time/residue: 0.2120 time to fit residues: 63.4094 Evaluate side-chains 220 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 312 CYS Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.204276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160533 restraints weight = 10455.703| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.48 r_work: 0.3769 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8871 Z= 0.221 Angle : 0.654 8.325 12035 Z= 0.337 Chirality : 0.044 0.290 1398 Planarity : 0.004 0.043 1505 Dihedral : 4.935 25.260 1224 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.92 % Allowed : 20.86 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1113 helix: 1.83 (0.27), residues: 341 sheet: -0.74 (0.33), residues: 255 loop : -1.13 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.003 0.001 HIS R 393 PHE 0.035 0.002 PHE R 439 TYR 0.024 0.001 TYR A 296 ARG 0.007 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4597.35 seconds wall clock time: 81 minutes 43.75 seconds (4903.75 seconds total)