Starting phenix.real_space_refine on Sun Jul 27 03:33:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vcb_21147/07_2025/6vcb_21147_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vcb_21147/07_2025/6vcb_21147.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/6vcb_21147/07_2025/6vcb_21147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vcb_21147/07_2025/6vcb_21147.map" model { file = "/net/cci-nas-00/data/ceres_data/6vcb_21147/07_2025/6vcb_21147_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vcb_21147/07_2025/6vcb_21147_neut.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= 0.004 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 Cl 2 4.86 5 C 5787 2.51 5 N 1573 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9074 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3000 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 3 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 231 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 30} 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: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1810 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'QW7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.55, per 1000 atoms: 0.61 Number of scatterers: 9074 At special positions: 0 Unit cell: (166.4, 102.96, 98.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 54 16.00 O 1658 8.00 N 1573 7.00 C 5787 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=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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=2.03 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: 2.23 Conformation dependent library (CDL) restraints added in 990.8 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 42.1% alpha, 17.6% 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 51 removed outlier: 3.917A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 4.439A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 removed outlier: 3.681A pdb=" N LEU R 142 " --> pdb=" O GLU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 206 Processing helix chain 'R' and resid 216 through 223 removed outlier: 3.898A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 256 Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.638A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 291 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 336 removed outlier: 4.504A 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 362 through 368 removed outlier: 3.691A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 393 removed outlier: 4.028A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 406 through 421 Processing helix chain 'P' and resid 8 through 34 removed outlier: 3.681A pdb=" N LYS P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.770A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.115A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.836A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.587A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.575A pdb=" N GLN B 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 4.116A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.646A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.606A 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: 4.094A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 79 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.861A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.747A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.040A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.741A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.707A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.893A 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 Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.495A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.259A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.450A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1314 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: 2.51 Time building geometry restraints manager: 2.59 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: 2908 1.34 - 1.46: 2128 1.46 - 1.58: 4167 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9277 Sorted by residual: bond pdb=" C17 QW7 R 501 " pdb=" C18 QW7 R 501 " ideal model delta sigma weight residual 1.490 1.391 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CG LEU R 159 " pdb=" CD1 LEU R 159 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.06e+00 bond pdb=" C03 QW7 R 501 " pdb=" O02 QW7 R 501 " ideal model delta sigma weight residual 1.349 1.400 -0.051 2.00e-02 2.50e+03 6.61e+00 bond pdb=" CG LEU R 159 " pdb=" CD2 LEU R 159 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.08e+00 bond pdb=" C26 QW7 R 501 " pdb=" C27 QW7 R 501 " ideal model delta sigma weight residual 1.528 1.483 0.045 2.00e-02 2.50e+03 5.02e+00 ... (remaining 9272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 12449 3.65 - 7.30: 125 7.30 - 10.95: 16 10.95 - 14.60: 2 14.60 - 18.25: 1 Bond angle restraints: 12593 Sorted by residual: angle pdb=" CA LEU A 46 " pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " ideal model delta sigma weight residual 116.30 134.55 -18.25 3.50e+00 8.16e-02 2.72e+01 angle pdb=" C ARG R 299 " pdb=" N ASN R 300 " pdb=" CA ASN R 300 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 130.74 -14.44 3.50e+00 8.16e-02 1.70e+01 angle pdb=" C ILE R 147 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " ideal model delta sigma weight residual 121.14 114.24 6.90 1.75e+00 3.27e-01 1.56e+01 ... (remaining 12588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 5047 15.42 - 30.84: 317 30.84 - 46.26: 89 46.26 - 61.68: 12 61.68 - 77.11: 8 Dihedral angle restraints: 5473 sinusoidal: 2106 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 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 93.00 145.59 -52.59 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 5470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1046 0.063 - 0.126: 305 0.126 - 0.190: 36 0.190 - 0.253: 12 0.253 - 0.316: 5 Chirality restraints: 1404 Sorted by residual: chirality pdb=" C09 QW7 R 501 " pdb=" C08 QW7 R 501 " pdb=" C10 QW7 R 501 " pdb=" N11 QW7 R 501 " both_signs ideal model delta sigma weight residual False -2.29 -2.60 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CG LEU A 44 " pdb=" CB LEU A 44 " pdb=" CD1 LEU A 44 " pdb=" CD2 LEU A 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU R 183 " pdb=" CB LEU R 183 " pdb=" CD1 LEU R 183 " pdb=" CD2 LEU R 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1401 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 242 " -0.018 2.00e-02 2.50e+03 1.75e-02 6.10e+00 pdb=" CG TYR R 242 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR R 242 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR R 242 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR R 242 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 242 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 169 " 0.021 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP B 169 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 169 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 169 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 282 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO R 283 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " -0.033 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 192 2.67 - 3.23: 8324 3.23 - 3.79: 14865 3.79 - 4.34: 19328 4.34 - 4.90: 31834 Nonbonded interactions: 74543 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.117 3.040 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.145 3.120 nonbonded pdb=" OE2 GLU N 6 " pdb=" N GLY N 121 " model vdw 2.159 3.120 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.160 3.120 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.222 3.040 ... (remaining 74538 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: 0.770 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.720 Find NCS groups from input model: 0.120 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 9283 Z= 0.284 Angle : 1.007 18.255 12605 Z= 0.532 Chirality : 0.061 0.316 1404 Planarity : 0.007 0.058 1599 Dihedral : 11.588 77.105 3275 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.85 % Allowed : 5.32 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.19), residues: 1130 helix: -2.61 (0.17), residues: 456 sheet: -2.38 (0.30), residues: 218 loop : -3.17 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 169 HIS 0.010 0.002 HIS B 142 PHE 0.021 0.003 PHE R 280 TYR 0.041 0.004 TYR R 242 ARG 0.010 0.001 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.11091 ( 464) hydrogen bonds : angle 6.70915 ( 1314) SS BOND : bond 0.00437 ( 6) SS BOND : angle 1.77997 ( 12) covalent geometry : bond 0.00655 ( 9277) covalent geometry : angle 1.00638 (12593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 267 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7641 (tp30) cc_final: 0.7356 (mt-10) REVERT: R 304 ASN cc_start: 0.7541 (m-40) cc_final: 0.6142 (t0) REVERT: R 372 ASP cc_start: 0.8600 (m-30) cc_final: 0.7942 (m-30) REVERT: R 417 TRP cc_start: 0.6373 (t-100) cc_final: 0.6064 (t-100) REVERT: P 18 SER cc_start: 0.8125 (m) cc_final: 0.7827 (p) REVERT: P 27 GLU cc_start: 0.7702 (tt0) cc_final: 0.7387 (tt0) REVERT: A 338 LYS cc_start: 0.8594 (ttpm) cc_final: 0.8278 (ttpp) REVERT: B 211 TRP cc_start: 0.8795 (m100) cc_final: 0.8570 (m100) REVERT: B 335 PHE cc_start: 0.7892 (m-80) cc_final: 0.7673 (m-10) REVERT: G 19 LEU cc_start: 0.8822 (mt) cc_final: 0.8493 (mt) REVERT: G 46 LYS cc_start: 0.8561 (mppt) cc_final: 0.8351 (mmtm) REVERT: G 48 ASP cc_start: 0.8561 (t70) cc_final: 0.8201 (t0) REVERT: N 82 GLN cc_start: 0.7274 (tp-100) cc_final: 0.7039 (tp-100) REVERT: N 105 ARG cc_start: 0.6366 (mtp-110) cc_final: 0.6160 (mtp-110) outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 0.2656 time to fit residues: 94.5134 Evaluate side-chains 171 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain A residue 43 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN R 47 GLN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 374 HIS A 14 ASN A 264 ASN B 155 ASN B 266 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 120 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128411 restraints weight = 12414.536| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.62 r_work: 0.3517 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9283 Z= 0.131 Angle : 0.645 11.443 12605 Z= 0.335 Chirality : 0.044 0.170 1404 Planarity : 0.004 0.037 1599 Dihedral : 6.011 53.884 1286 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.19 % Allowed : 11.18 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.22), residues: 1130 helix: -0.70 (0.22), residues: 472 sheet: -1.98 (0.32), residues: 197 loop : -2.77 (0.23), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 297 HIS 0.004 0.001 HIS A 220 PHE 0.023 0.001 PHE R 280 TYR 0.019 0.002 TYR R 88 ARG 0.006 0.001 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 464) hydrogen bonds : angle 5.27146 ( 1314) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.96926 ( 12) covalent geometry : bond 0.00285 ( 9277) covalent geometry : angle 0.64478 (12593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 211 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7851 (tp30) cc_final: 0.7218 (mt-10) REVERT: R 299 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7679 (mmm160) REVERT: R 304 ASN cc_start: 0.7372 (m-40) cc_final: 0.5984 (t0) REVERT: A 33 ASP cc_start: 0.7915 (m-30) cc_final: 0.7684 (m-30) REVERT: A 264 ASN cc_start: 0.8343 (t0) cc_final: 0.8095 (t0) REVERT: A 310 ASP cc_start: 0.7177 (m-30) cc_final: 0.6905 (p0) REVERT: A 338 LYS cc_start: 0.8436 (ttpm) cc_final: 0.8020 (ttpp) REVERT: B 10 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 12 GLU cc_start: 0.8635 (tp30) cc_final: 0.8415 (tp30) REVERT: B 14 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7314 (tt) REVERT: B 85 TYR cc_start: 0.7345 (m-80) cc_final: 0.7137 (m-10) REVERT: B 211 TRP cc_start: 0.8970 (m100) cc_final: 0.8760 (m100) REVERT: B 219 ARG cc_start: 0.8367 (ptp-110) cc_final: 0.8090 (ptp-170) REVERT: B 280 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7834 (tptp) REVERT: G 48 ASP cc_start: 0.8540 (t70) cc_final: 0.8271 (t0) REVERT: N 60 TYR cc_start: 0.8608 (m-10) cc_final: 0.8371 (m-10) REVERT: N 82 GLN cc_start: 0.7479 (tp-100) cc_final: 0.7143 (tp-100) REVERT: N 83 MET cc_start: 0.7120 (mtt) cc_final: 0.6766 (mtt) REVERT: N 98 ARG cc_start: 0.8391 (ptt90) cc_final: 0.8018 (ptm-80) outliers start: 30 outliers final: 17 residues processed: 231 average time/residue: 0.2181 time to fit residues: 68.8923 Evaluate side-chains 188 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 210 GLN R 221 GLN ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 371 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122090 restraints weight = 12465.123| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.63 r_work: 0.3424 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9283 Z= 0.222 Angle : 0.689 10.231 12605 Z= 0.358 Chirality : 0.046 0.218 1404 Planarity : 0.004 0.037 1599 Dihedral : 5.755 56.986 1286 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.73 % Allowed : 14.59 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.23), residues: 1130 helix: -0.04 (0.24), residues: 469 sheet: -2.04 (0.31), residues: 214 loop : -2.51 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 243 HIS 0.006 0.002 HIS A 220 PHE 0.029 0.002 PHE B 199 TYR 0.023 0.002 TYR R 242 ARG 0.006 0.001 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 464) hydrogen bonds : angle 5.07648 ( 1314) SS BOND : bond 0.00237 ( 6) SS BOND : angle 1.07939 ( 12) covalent geometry : bond 0.00510 ( 9277) covalent geometry : angle 0.68854 (12593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7207 (tp) REVERT: R 202 LYS cc_start: 0.7833 (tptm) cc_final: 0.7570 (tptt) REVERT: R 262 GLU cc_start: 0.8190 (tp30) cc_final: 0.7239 (pm20) REVERT: R 304 ASN cc_start: 0.7300 (m-40) cc_final: 0.5757 (t0) REVERT: R 369 PHE cc_start: 0.4896 (t80) cc_final: 0.3791 (t80) REVERT: R 373 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: A 360 TYR cc_start: 0.8887 (m-10) cc_final: 0.8654 (m-10) REVERT: B 10 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7963 (tm-30) REVERT: B 12 GLU cc_start: 0.8695 (tp30) cc_final: 0.8447 (tp30) REVERT: B 200 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8771 (p) REVERT: B 219 ARG cc_start: 0.8405 (ptp-110) cc_final: 0.8004 (ptp-170) REVERT: B 334 SER cc_start: 0.8982 (m) cc_final: 0.8758 (m) REVERT: G 19 LEU cc_start: 0.8543 (mt) cc_final: 0.8311 (mt) REVERT: N 118 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.8520 (mtm-85) outliers start: 35 outliers final: 24 residues processed: 204 average time/residue: 0.2492 time to fit residues: 68.2232 Evaluate side-chains 184 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 0.0000 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** 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 = 0.3941 r_free = 0.3941 target = 0.157369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123664 restraints weight = 12476.758| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.71 r_work: 0.3436 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9283 Z= 0.148 Angle : 0.608 8.093 12605 Z= 0.315 Chirality : 0.044 0.231 1404 Planarity : 0.004 0.036 1599 Dihedral : 5.409 49.175 1285 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.94 % Allowed : 16.51 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1130 helix: 0.37 (0.24), residues: 470 sheet: -1.85 (0.32), residues: 211 loop : -2.21 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE B 199 TYR 0.014 0.002 TYR R 242 ARG 0.009 0.000 ARG R 227 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 464) hydrogen bonds : angle 4.86331 ( 1314) SS BOND : bond 0.00186 ( 6) SS BOND : angle 0.87996 ( 12) covalent geometry : bond 0.00339 ( 9277) covalent geometry : angle 0.60747 (12593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7927 (tp30) cc_final: 0.7216 (pm20) REVERT: R 291 TYR cc_start: 0.7901 (m-10) cc_final: 0.7662 (m-10) REVERT: R 304 ASN cc_start: 0.7370 (m-40) cc_final: 0.5912 (t0) REVERT: R 369 PHE cc_start: 0.4981 (t80) cc_final: 0.3824 (t80) REVERT: R 373 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: A 360 TYR cc_start: 0.8817 (m-10) cc_final: 0.8495 (m-10) REVERT: B 10 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 12 GLU cc_start: 0.8756 (tp30) cc_final: 0.8521 (tp30) REVERT: B 211 TRP cc_start: 0.8999 (m100) cc_final: 0.8586 (m100) REVERT: B 334 SER cc_start: 0.8795 (m) cc_final: 0.8595 (m) REVERT: N 82 GLN cc_start: 0.7630 (tp-100) cc_final: 0.7404 (tp-100) REVERT: N 105 ARG cc_start: 0.6624 (mtp-110) cc_final: 0.6274 (mtp-110) outliers start: 37 outliers final: 21 residues processed: 194 average time/residue: 0.2926 time to fit residues: 79.8003 Evaluate side-chains 181 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 371 MET Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 92 optimal weight: 0.0270 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** 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 = 0.3945 r_free = 0.3945 target = 0.157873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123925 restraints weight = 12591.326| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.75 r_work: 0.3441 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9283 Z= 0.143 Angle : 0.607 11.417 12605 Z= 0.312 Chirality : 0.044 0.246 1404 Planarity : 0.004 0.056 1599 Dihedral : 4.997 37.237 1283 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.47 % Allowed : 17.78 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1130 helix: 0.73 (0.25), residues: 464 sheet: -1.65 (0.33), residues: 221 loop : -2.03 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE P 28 TYR 0.014 0.002 TYR R 242 ARG 0.005 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 464) hydrogen bonds : angle 4.74398 ( 1314) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.78977 ( 12) covalent geometry : bond 0.00329 ( 9277) covalent geometry : angle 0.60694 (12593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.8767 (tp30) cc_final: 0.8132 (tp30) REVERT: R 262 GLU cc_start: 0.7973 (tp30) cc_final: 0.7300 (pm20) REVERT: R 291 TYR cc_start: 0.7919 (m-10) cc_final: 0.7703 (m-10) REVERT: R 304 ASN cc_start: 0.7355 (m-40) cc_final: 0.5942 (t0) REVERT: R 369 PHE cc_start: 0.5105 (t80) cc_final: 0.3884 (t80) REVERT: R 373 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: A 270 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8655 (mp) REVERT: A 360 TYR cc_start: 0.8798 (m-10) cc_final: 0.8521 (m-10) REVERT: B 10 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8000 (tm-30) REVERT: B 12 GLU cc_start: 0.8773 (tp30) cc_final: 0.8534 (tp30) REVERT: B 211 TRP cc_start: 0.9008 (m100) cc_final: 0.8521 (m100) REVERT: N 82 GLN cc_start: 0.7627 (tp-100) cc_final: 0.7402 (tp40) REVERT: N 105 ARG cc_start: 0.6553 (mtp-110) cc_final: 0.6230 (mtp-110) outliers start: 42 outliers final: 28 residues processed: 201 average time/residue: 0.2094 time to fit residues: 59.7381 Evaluate side-chains 190 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 88 optimal weight: 0.0770 chunk 44 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125101 restraints weight = 12256.067| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.56 r_work: 0.3457 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9283 Z= 0.154 Angle : 0.603 7.123 12605 Z= 0.313 Chirality : 0.044 0.253 1404 Planarity : 0.004 0.052 1599 Dihedral : 4.928 37.017 1283 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.47 % Allowed : 18.32 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.25), residues: 1130 helix: 0.83 (0.24), residues: 466 sheet: -1.59 (0.34), residues: 214 loop : -1.81 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE P 28 TYR 0.014 0.002 TYR R 242 ARG 0.007 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 464) hydrogen bonds : angle 4.66836 ( 1314) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.77857 ( 12) covalent geometry : bond 0.00356 ( 9277) covalent geometry : angle 0.60284 (12593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.8774 (tp30) cc_final: 0.8220 (tp30) REVERT: R 192 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7090 (tp) REVERT: R 262 GLU cc_start: 0.8102 (tp30) cc_final: 0.7302 (pm20) REVERT: R 289 TYR cc_start: 0.8191 (t80) cc_final: 0.7857 (t80) REVERT: R 291 TYR cc_start: 0.7939 (m-10) cc_final: 0.7726 (m-10) REVERT: R 304 ASN cc_start: 0.7323 (m-40) cc_final: 0.5981 (t0) REVERT: R 369 PHE cc_start: 0.5127 (t80) cc_final: 0.3860 (t80) REVERT: R 373 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: A 270 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8555 (mp) REVERT: A 310 ASP cc_start: 0.7136 (m-30) cc_final: 0.6871 (p0) REVERT: A 360 TYR cc_start: 0.8791 (m-10) cc_final: 0.8400 (m-10) REVERT: B 10 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 12 GLU cc_start: 0.8755 (tp30) cc_final: 0.8498 (tp30) REVERT: B 211 TRP cc_start: 0.9036 (m100) cc_final: 0.8490 (m100) outliers start: 42 outliers final: 28 residues processed: 196 average time/residue: 0.2070 time to fit residues: 56.8488 Evaluate side-chains 190 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 371 MET Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 0.0030 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125321 restraints weight = 12604.738| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.63 r_work: 0.3462 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9283 Z= 0.119 Angle : 0.595 10.307 12605 Z= 0.305 Chirality : 0.043 0.261 1404 Planarity : 0.004 0.044 1599 Dihedral : 4.735 34.008 1283 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.19 % Allowed : 20.77 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.25), residues: 1130 helix: 1.01 (0.25), residues: 468 sheet: -1.43 (0.34), residues: 220 loop : -1.71 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE P 28 TYR 0.013 0.001 TYR R 145 ARG 0.007 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 464) hydrogen bonds : angle 4.57743 ( 1314) SS BOND : bond 0.00202 ( 6) SS BOND : angle 0.76372 ( 12) covalent geometry : bond 0.00264 ( 9277) covalent geometry : angle 0.59439 (12593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.8779 (tp30) cc_final: 0.8236 (tp30) REVERT: R 262 GLU cc_start: 0.7934 (tp30) cc_final: 0.7304 (pm20) REVERT: R 291 TYR cc_start: 0.7888 (m-10) cc_final: 0.7646 (m-10) REVERT: R 304 ASN cc_start: 0.7482 (m-40) cc_final: 0.6190 (t0) REVERT: R 369 PHE cc_start: 0.5340 (t80) cc_final: 0.4109 (t80) REVERT: R 373 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: A 270 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 10 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 12 GLU cc_start: 0.8799 (tp30) cc_final: 0.8551 (tp30) outliers start: 30 outliers final: 23 residues processed: 199 average time/residue: 0.2355 time to fit residues: 62.9943 Evaluate side-chains 191 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 371 MET Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 64 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128358 restraints weight = 12588.351| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.58 r_work: 0.3493 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9283 Z= 0.112 Angle : 0.593 7.829 12605 Z= 0.304 Chirality : 0.043 0.273 1404 Planarity : 0.004 0.044 1599 Dihedral : 4.505 34.098 1281 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.51 % Allowed : 19.91 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1130 helix: 1.22 (0.25), residues: 465 sheet: -1.22 (0.34), residues: 220 loop : -1.63 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE P 28 TYR 0.020 0.001 TYR R 289 ARG 0.006 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 464) hydrogen bonds : angle 4.49296 ( 1314) SS BOND : bond 0.00235 ( 6) SS BOND : angle 0.69383 ( 12) covalent geometry : bond 0.00245 ( 9277) covalent geometry : angle 0.59241 (12593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 41 GLU cc_start: 0.8779 (tp30) cc_final: 0.8251 (tp30) REVERT: R 262 GLU cc_start: 0.7930 (tp30) cc_final: 0.7348 (pm20) REVERT: R 304 ASN cc_start: 0.7569 (m-40) cc_final: 0.6345 (t0) REVERT: R 369 PHE cc_start: 0.5229 (t80) cc_final: 0.4035 (t80) REVERT: R 373 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: A 270 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8545 (mp) REVERT: B 10 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 12 GLU cc_start: 0.8803 (tp30) cc_final: 0.8555 (tp30) REVERT: B 211 TRP cc_start: 0.8948 (m100) cc_final: 0.8588 (m-10) outliers start: 33 outliers final: 20 residues processed: 191 average time/residue: 0.2053 time to fit residues: 54.5583 Evaluate side-chains 178 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.0970 chunk 8 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127937 restraints weight = 12436.631| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.56 r_work: 0.3483 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9283 Z= 0.122 Angle : 0.610 13.546 12605 Z= 0.310 Chirality : 0.044 0.281 1404 Planarity : 0.004 0.043 1599 Dihedral : 4.457 31.845 1281 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.88 % Allowed : 21.09 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1130 helix: 1.28 (0.25), residues: 465 sheet: -1.17 (0.34), residues: 225 loop : -1.50 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP R 297 HIS 0.005 0.001 HIS B 311 PHE 0.017 0.001 PHE P 28 TYR 0.016 0.001 TYR N 60 ARG 0.004 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 464) hydrogen bonds : angle 4.47946 ( 1314) SS BOND : bond 0.00222 ( 6) SS BOND : angle 0.71928 ( 12) covalent geometry : bond 0.00274 ( 9277) covalent geometry : angle 0.60991 (12593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7969 (tp30) cc_final: 0.7368 (pm20) REVERT: R 303 MET cc_start: 0.8342 (mmt) cc_final: 0.7668 (mmt) REVERT: R 304 ASN cc_start: 0.7527 (m-40) cc_final: 0.6329 (t0) REVERT: R 373 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: A 270 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8527 (mp) REVERT: B 10 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8042 (tm-30) REVERT: B 12 GLU cc_start: 0.8776 (tp30) cc_final: 0.8558 (tp30) REVERT: B 211 TRP cc_start: 0.8966 (m100) cc_final: 0.8584 (m-10) REVERT: N 74 ASN cc_start: 0.8777 (p0) cc_final: 0.8406 (p0) outliers start: 27 outliers final: 20 residues processed: 182 average time/residue: 0.1967 time to fit residues: 50.3896 Evaluate side-chains 180 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 chunk 87 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 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 = 0.3962 r_free = 0.3962 target = 0.159161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125466 restraints weight = 12633.105| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.61 r_work: 0.3460 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9283 Z= 0.145 Angle : 0.634 14.895 12605 Z= 0.322 Chirality : 0.045 0.283 1404 Planarity : 0.004 0.044 1599 Dihedral : 4.535 32.983 1281 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.56 % Allowed : 22.26 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1130 helix: 1.21 (0.25), residues: 465 sheet: -1.21 (0.34), residues: 225 loop : -1.44 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP R 297 HIS 0.005 0.001 HIS B 311 PHE 0.017 0.001 PHE P 28 TYR 0.024 0.002 TYR R 289 ARG 0.006 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 464) hydrogen bonds : angle 4.47927 ( 1314) SS BOND : bond 0.00244 ( 6) SS BOND : angle 0.72214 ( 12) covalent geometry : bond 0.00335 ( 9277) covalent geometry : angle 0.63378 (12593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7984 (tp30) cc_final: 0.7374 (pm20) REVERT: R 303 MET cc_start: 0.8246 (mmt) cc_final: 0.7634 (mmt) REVERT: R 304 ASN cc_start: 0.7531 (m-40) cc_final: 0.6352 (t0) REVERT: R 373 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: A 270 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8536 (mp) REVERT: B 10 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8196 (tm-30) REVERT: B 12 GLU cc_start: 0.8762 (tp30) cc_final: 0.8499 (tp30) REVERT: B 289 TYR cc_start: 0.8844 (m-10) cc_final: 0.8633 (m-10) REVERT: N 74 ASN cc_start: 0.8800 (p0) cc_final: 0.8431 (p0) outliers start: 24 outliers final: 21 residues processed: 181 average time/residue: 0.2103 time to fit residues: 53.2690 Evaluate side-chains 182 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 371 MET Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 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 = 0.3992 r_free = 0.3992 target = 0.162026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128664 restraints weight = 12454.094| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.59 r_work: 0.3489 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9283 Z= 0.123 Angle : 0.629 15.094 12605 Z= 0.320 Chirality : 0.044 0.282 1404 Planarity : 0.004 0.050 1599 Dihedral : 4.448 33.390 1281 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.45 % Allowed : 22.47 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1130 helix: 1.29 (0.25), residues: 465 sheet: -1.12 (0.34), residues: 225 loop : -1.40 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP R 297 HIS 0.006 0.001 HIS B 311 PHE 0.018 0.001 PHE P 28 TYR 0.015 0.001 TYR B 289 ARG 0.006 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 464) hydrogen bonds : angle 4.43866 ( 1314) SS BOND : bond 0.00217 ( 6) SS BOND : angle 0.74603 ( 12) covalent geometry : bond 0.00277 ( 9277) covalent geometry : angle 0.62916 (12593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4580.28 seconds wall clock time: 81 minutes 39.21 seconds (4899.21 seconds total)