Starting phenix.real_space_refine on Sat Aug 23 01:09:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ija_35483/08_2025/8ija_35483_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ija_35483/08_2025/8ija_35483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ija_35483/08_2025/8ija_35483_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ija_35483/08_2025/8ija_35483_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ija_35483/08_2025/8ija_35483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ija_35483/08_2025/8ija_35483.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 5653 2.51 5 N 1506 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8845 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2357 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1699 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.25 Number of scatterers: 8845 At special positions: 0 Unit cell: (87.15, 119.52, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 1619 8.00 N 1506 7.00 C 5653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 321.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 16 sheets defined 36.4% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 23 through 55 removed outlier: 3.740A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.610A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 89 removed outlier: 3.646A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.836A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 131 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.705A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 158 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 188 through 218 removed outlier: 3.762A pdb=" N LEU A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 262 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 271 through 294 removed outlier: 3.689A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'C' and resid 6 through 32 removed outlier: 3.606A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.715A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.233A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.507A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 330 through 352 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.705A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA3, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.301A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.552A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.560A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.470A 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: 3.687A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.981A 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: 4.138A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.726A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.738A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.758A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.823A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.823A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1260 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: 1.14 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2656 1.34 - 1.46: 2304 1.46 - 1.59: 3981 1.59 - 1.71: 0 1.71 - 1.84: 97 Bond restraints: 9038 Sorted by residual: bond pdb=" ND1 HIS A 9 " pdb=" CE1 HIS A 9 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.83e+01 bond pdb=" ND1 HIS A 259 " pdb=" CE1 HIS A 259 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.78e+01 bond pdb=" CG ASN A 17 " pdb=" OD1 ASN A 17 " ideal model delta sigma weight residual 1.231 1.329 -0.098 1.90e-02 2.77e+03 2.65e+01 bond pdb=" ND1 HIS A 133 " pdb=" CE1 HIS A 133 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.64e+01 bond pdb=" CD2 HIS A 133 " pdb=" NE2 HIS A 133 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.10e-02 8.26e+03 2.37e+01 ... (remaining 9033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.90: 12206 6.90 - 13.80: 22 13.80 - 20.71: 7 20.71 - 27.61: 5 27.61 - 34.51: 2 Bond angle restraints: 12242 Sorted by residual: angle pdb=" N TYR A 295 " pdb=" CA TYR A 295 " pdb=" C TYR A 295 " ideal model delta sigma weight residual 111.69 146.20 -34.51 1.23e+00 6.61e-01 7.87e+02 angle pdb=" N THR C 324 " pdb=" CA THR C 324 " pdb=" C THR C 324 " ideal model delta sigma weight residual 111.24 142.05 -30.81 1.29e+00 6.01e-01 5.70e+02 angle pdb=" N CYS C 325 " pdb=" CA CYS C 325 " pdb=" C CYS C 325 " ideal model delta sigma weight residual 112.86 134.01 -21.15 1.22e+00 6.72e-01 3.01e+02 angle pdb=" C VAL C 201 " pdb=" CA VAL C 201 " pdb=" CB VAL C 201 " ideal model delta sigma weight residual 111.81 91.92 19.89 1.37e+00 5.33e-01 2.11e+02 angle pdb=" N PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta sigma weight residual 110.33 89.57 20.76 1.50e+00 4.44e-01 1.91e+02 ... (remaining 12237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4517 17.82 - 35.64: 590 35.64 - 53.47: 179 53.47 - 71.29: 33 71.29 - 89.11: 18 Dihedral angle restraints: 5337 sinusoidal: 2050 harmonic: 3287 Sorted by residual: dihedral pdb=" C VAL C 201 " pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" CB VAL C 201 " ideal model delta harmonic sigma weight residual -122.00 -90.73 -31.27 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" N PHE A 296 " pdb=" C PHE A 296 " pdb=" CA PHE A 296 " pdb=" CB PHE A 296 " ideal model delta harmonic sigma weight residual 122.80 95.32 27.48 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C CYS C 325 " pdb=" N CYS C 325 " pdb=" CA CYS C 325 " pdb=" CB CYS C 325 " ideal model delta harmonic sigma weight residual -122.60 -143.50 20.90 0 2.50e+00 1.60e-01 6.99e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.260: 1375 0.260 - 0.519: 5 0.519 - 0.778: 2 0.778 - 1.038: 0 1.038 - 1.297: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA TYR A 295 " pdb=" N TYR A 295 " pdb=" C TYR A 295 " pdb=" CB TYR A 295 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.21e+01 chirality pdb=" CA ARG A 270 " pdb=" N ARG A 270 " pdb=" C ARG A 270 " pdb=" CB ARG A 270 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.21e+01 chirality pdb=" CA CYS C 325 " pdb=" N CYS C 325 " pdb=" C CYS C 325 " pdb=" CB CYS C 325 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.94e+01 ... (remaining 1383 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.111 2.00e-02 2.50e+03 6.51e-02 8.49e+01 pdb=" CG TYR A 284 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 91 " -0.099 2.00e-02 2.50e+03 5.25e-02 6.89e+01 pdb=" CG TRP A 91 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 91 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP A 91 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 91 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 91 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 91 " 0.066 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 91 " -0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 91 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP A 91 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 87 " 0.062 2.00e-02 2.50e+03 3.17e-02 2.01e+01 pdb=" CG TYR A 87 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 87 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 87 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 87 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 87 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 87 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 87 " 0.035 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 51 2.41 - 3.04: 5361 3.04 - 3.66: 13377 3.66 - 4.28: 21213 4.28 - 4.90: 35863 Nonbonded interactions: 75865 Sorted by model distance: nonbonded pdb=" O THR C 324 " pdb=" CG2 THR C 327 " model vdw 1.793 3.460 nonbonded pdb=" O ARG A 270 " pdb=" NH1 ARG A 270 " model vdw 1.900 3.120 nonbonded pdb=" O VAL C 201 " pdb=" CG2 VAL C 201 " model vdw 1.912 3.460 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.046 3.040 nonbonded pdb=" OG SER A 298 " pdb=" O GLY C 352 " model vdw 2.049 3.040 ... (remaining 75860 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.005 0.098 9043 Z= 0.279 Angle : 1.105 34.511 12252 Z= 0.714 Chirality : 0.084 1.297 1386 Planarity : 0.005 0.065 1548 Dihedral : 18.233 89.108 3198 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 5.37 % Allowed : 27.37 % Favored : 67.26 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.26), residues: 1118 helix: 1.55 (0.27), residues: 376 sheet: -0.03 (0.30), residues: 281 loop : -1.06 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 148 TYR 0.111 0.003 TYR A 284 PHE 0.023 0.002 PHE A 276 TRP 0.099 0.003 TRP A 91 HIS 0.010 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 9038) covalent geometry : angle 1.10463 (12242) SS BOND : bond 0.00421 ( 5) SS BOND : angle 1.50365 ( 10) hydrogen bonds : bond 0.12506 ( 444) hydrogen bonds : angle 6.40692 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 141 time to evaluate : 0.257 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 38 PHE cc_start: 0.6715 (t80) cc_final: 0.6493 (t80) REVERT: A 79 CYS cc_start: 0.7974 (m) cc_final: 0.7618 (m) REVERT: A 156 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7274 (mm) REVERT: A 258 LEU cc_start: 0.7171 (pp) cc_final: 0.6332 (mt) REVERT: C 309 ASP cc_start: 0.8273 (m-30) cc_final: 0.7952 (m-30) REVERT: B 46 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7630 (mpt180) outliers start: 51 outliers final: 43 residues processed: 185 average time/residue: 0.4865 time to fit residues: 95.8775 Evaluate side-chains 172 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 128 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 86 ASN A 133 HIS C 188 HIS G 59 ASN S 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.100322 restraints weight = 10524.522| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.33 r_work: 0.2995 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9043 Z= 0.183 Angle : 0.598 6.392 12252 Z= 0.315 Chirality : 0.044 0.193 1386 Planarity : 0.004 0.048 1548 Dihedral : 8.088 58.888 1291 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 6.42 % Allowed : 24.32 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1118 helix: 1.73 (0.27), residues: 384 sheet: 0.11 (0.30), residues: 285 loop : -1.14 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 168 TYR 0.016 0.001 TYR S 178 PHE 0.019 0.002 PHE A 38 TRP 0.011 0.001 TRP A 93 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9038) covalent geometry : angle 0.59816 (12242) SS BOND : bond 0.00407 ( 5) SS BOND : angle 0.88006 ( 10) hydrogen bonds : bond 0.04356 ( 444) hydrogen bonds : angle 4.90634 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 0.276 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 34 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5504 (mp) REVERT: A 79 CYS cc_start: 0.7904 (m) cc_final: 0.7570 (m) REVERT: A 80 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6907 (mm) REVERT: A 110 ASN cc_start: 0.8165 (m-40) cc_final: 0.7515 (m-40) REVERT: C 209 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8635 (pttm) REVERT: B 268 ASN cc_start: 0.8179 (t0) cc_final: 0.7766 (t0) REVERT: S 135 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7677 (m) outliers start: 61 outliers final: 28 residues processed: 176 average time/residue: 0.5266 time to fit residues: 98.6574 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 325 CYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 72 ARG Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 138 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN C 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.102383 restraints weight = 10402.767| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.31 r_work: 0.3030 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9043 Z= 0.137 Angle : 0.556 7.086 12252 Z= 0.290 Chirality : 0.042 0.157 1386 Planarity : 0.004 0.044 1548 Dihedral : 6.799 54.555 1251 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.26 % Allowed : 25.47 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.26), residues: 1118 helix: 1.83 (0.27), residues: 386 sheet: 0.12 (0.31), residues: 286 loop : -1.15 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.016 0.001 TYR S 178 PHE 0.015 0.001 PHE C 189 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 259 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9038) covalent geometry : angle 0.55541 (12242) SS BOND : bond 0.00322 ( 5) SS BOND : angle 0.89863 ( 10) hydrogen bonds : bond 0.03897 ( 444) hydrogen bonds : angle 4.62335 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.289 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7407 (tttt) cc_final: 0.7006 (mtpm) REVERT: A 34 LEU cc_start: 0.5584 (OUTLIER) cc_final: 0.5360 (mp) REVERT: A 79 CYS cc_start: 0.7977 (m) cc_final: 0.7733 (m) REVERT: A 80 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6838 (mm) REVERT: A 97 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5569 (t0) REVERT: A 164 LYS cc_start: 0.6296 (ptpt) cc_final: 0.6075 (ptpp) REVERT: A 257 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6613 (mp) REVERT: C 309 ASP cc_start: 0.8460 (m-30) cc_final: 0.8170 (m-30) REVERT: C 350 ASP cc_start: 0.8553 (m-30) cc_final: 0.8312 (m-30) REVERT: B 268 ASN cc_start: 0.8174 (t0) cc_final: 0.7775 (t0) REVERT: S 135 VAL cc_start: 0.7837 (OUTLIER) cc_final: 0.7635 (m) outliers start: 50 outliers final: 17 residues processed: 172 average time/residue: 0.5328 time to fit residues: 97.4992 Evaluate side-chains 154 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS B 32 GLN S 77 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.100892 restraints weight = 10550.342| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.34 r_work: 0.3005 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9043 Z= 0.168 Angle : 0.572 7.287 12252 Z= 0.298 Chirality : 0.043 0.174 1386 Planarity : 0.004 0.041 1548 Dihedral : 5.903 54.420 1236 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.26 % Allowed : 26.00 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.26), residues: 1118 helix: 1.85 (0.27), residues: 385 sheet: 0.08 (0.31), residues: 287 loop : -1.16 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 208 TYR 0.019 0.001 TYR A 269 PHE 0.021 0.001 PHE A 38 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9038) covalent geometry : angle 0.57160 (12242) SS BOND : bond 0.00302 ( 5) SS BOND : angle 0.89418 ( 10) hydrogen bonds : bond 0.03983 ( 444) hydrogen bonds : angle 4.61571 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.236 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7355 (tttt) cc_final: 0.7035 (mtpm) REVERT: A 34 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5551 (mp) REVERT: A 80 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6779 (mm) REVERT: A 97 ASP cc_start: 0.5888 (OUTLIER) cc_final: 0.5216 (OUTLIER) REVERT: A 227 LYS cc_start: 0.6640 (mmmm) cc_final: 0.6430 (mmmm) REVERT: A 257 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6598 (mp) REVERT: C 309 ASP cc_start: 0.8483 (m-30) cc_final: 0.8203 (m-30) REVERT: C 350 ASP cc_start: 0.8614 (m-30) cc_final: 0.8290 (m-30) REVERT: B 268 ASN cc_start: 0.8171 (t0) cc_final: 0.7772 (t0) REVERT: S 135 VAL cc_start: 0.7847 (OUTLIER) cc_final: 0.7637 (m) outliers start: 50 outliers final: 25 residues processed: 169 average time/residue: 0.5201 time to fit residues: 93.5093 Evaluate side-chains 159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100060 restraints weight = 10464.346| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.34 r_work: 0.2990 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9043 Z= 0.189 Angle : 0.585 8.242 12252 Z= 0.304 Chirality : 0.043 0.182 1386 Planarity : 0.004 0.041 1548 Dihedral : 5.852 55.328 1235 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.68 % Allowed : 26.21 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1118 helix: 1.81 (0.27), residues: 385 sheet: 0.04 (0.30), residues: 287 loop : -1.18 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 148 TYR 0.014 0.001 TYR S 178 PHE 0.015 0.002 PHE C 189 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9038) covalent geometry : angle 0.58484 (12242) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.02214 ( 10) hydrogen bonds : bond 0.04069 ( 444) hydrogen bonds : angle 4.62743 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 134 time to evaluate : 0.380 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 15 LYS cc_start: 0.5747 (tptt) cc_final: 0.5509 (tptt) REVERT: A 28 LYS cc_start: 0.7355 (tttt) cc_final: 0.7047 (mtpm) REVERT: A 34 LEU cc_start: 0.5732 (OUTLIER) cc_final: 0.5512 (mp) REVERT: A 80 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6924 (mm) REVERT: A 94 LYS cc_start: 0.7121 (pptt) cc_final: 0.6084 (mmmt) REVERT: A 166 LYS cc_start: 0.5677 (tppt) cc_final: 0.5368 (mmtm) REVERT: A 257 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6613 (mp) REVERT: C 209 LYS cc_start: 0.8812 (pttm) cc_final: 0.8344 (ptpp) REVERT: C 309 ASP cc_start: 0.8500 (m-30) cc_final: 0.8224 (m-30) REVERT: C 350 ASP cc_start: 0.8624 (m-30) cc_final: 0.8377 (m-30) REVERT: B 268 ASN cc_start: 0.8167 (t0) cc_final: 0.7779 (t0) REVERT: G 21 MET cc_start: 0.7636 (tpp) cc_final: 0.7343 (tpp) REVERT: S 135 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7700 (m) outliers start: 54 outliers final: 26 residues processed: 173 average time/residue: 0.5299 time to fit residues: 97.6204 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN B 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098199 restraints weight = 10509.254| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.34 r_work: 0.2963 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9043 Z= 0.254 Angle : 0.636 9.284 12252 Z= 0.330 Chirality : 0.046 0.198 1386 Planarity : 0.004 0.043 1548 Dihedral : 6.012 55.900 1234 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.58 % Allowed : 26.63 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1118 helix: 1.70 (0.27), residues: 384 sheet: -0.02 (0.30), residues: 287 loop : -1.21 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 148 TYR 0.019 0.002 TYR A 269 PHE 0.020 0.002 PHE A 38 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 9038) covalent geometry : angle 0.63483 (12242) SS BOND : bond 0.00454 ( 5) SS BOND : angle 1.20583 ( 10) hydrogen bonds : bond 0.04449 ( 444) hydrogen bonds : angle 4.79550 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 0.317 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 15 LYS cc_start: 0.5742 (tptt) cc_final: 0.5527 (tptt) REVERT: A 28 LYS cc_start: 0.7486 (tttt) cc_final: 0.7120 (mtpm) REVERT: A 80 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7081 (mm) REVERT: A 257 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6592 (mp) REVERT: C 309 ASP cc_start: 0.8512 (m-30) cc_final: 0.7990 (m-30) REVERT: C 350 ASP cc_start: 0.8558 (m-30) cc_final: 0.8324 (m-30) REVERT: B 17 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6434 (tt0) REVERT: B 46 ARG cc_start: 0.8539 (mtp-110) cc_final: 0.7920 (mpt180) REVERT: B 70 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9117 (pp) REVERT: S 135 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7655 (m) outliers start: 53 outliers final: 30 residues processed: 169 average time/residue: 0.5176 time to fit residues: 92.8490 Evaluate side-chains 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 0.0570 chunk 78 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.102558 restraints weight = 10573.016| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.34 r_work: 0.3027 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9043 Z= 0.127 Angle : 0.577 9.494 12252 Z= 0.296 Chirality : 0.042 0.155 1386 Planarity : 0.004 0.040 1548 Dihedral : 5.436 56.392 1233 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.89 % Allowed : 28.74 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.26), residues: 1118 helix: 1.86 (0.27), residues: 384 sheet: 0.01 (0.30), residues: 285 loop : -1.10 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.018 0.001 TYR S 178 PHE 0.014 0.001 PHE C 189 TRP 0.011 0.001 TRP S 47 HIS 0.002 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9038) covalent geometry : angle 0.57626 (12242) SS BOND : bond 0.00496 ( 5) SS BOND : angle 0.93912 ( 10) hydrogen bonds : bond 0.03702 ( 444) hydrogen bonds : angle 4.51765 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.374 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7379 (tttt) cc_final: 0.7052 (mtpm) REVERT: A 80 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6904 (mm) REVERT: A 94 LYS cc_start: 0.7063 (pptt) cc_final: 0.6072 (mmmt) REVERT: A 257 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6543 (mp) REVERT: A 258 LEU cc_start: 0.7030 (pp) cc_final: 0.6141 (mm) REVERT: C 209 LYS cc_start: 0.8820 (pttm) cc_final: 0.8343 (ptpp) REVERT: C 309 ASP cc_start: 0.8514 (m-30) cc_final: 0.8261 (m-30) REVERT: C 350 ASP cc_start: 0.8580 (m-30) cc_final: 0.8234 (m-30) REVERT: B 46 ARG cc_start: 0.8544 (mtp-110) cc_final: 0.7980 (mpt180) REVERT: B 268 ASN cc_start: 0.8200 (t0) cc_final: 0.7782 (t0) REVERT: G 21 MET cc_start: 0.7571 (tpp) cc_final: 0.7280 (tpp) REVERT: S 135 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7668 (m) outliers start: 37 outliers final: 21 residues processed: 166 average time/residue: 0.5197 time to fit residues: 91.9161 Evaluate side-chains 162 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.147142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101834 restraints weight = 10437.641| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.32 r_work: 0.3019 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9043 Z= 0.150 Angle : 0.592 10.320 12252 Z= 0.301 Chirality : 0.043 0.267 1386 Planarity : 0.004 0.040 1548 Dihedral : 5.100 45.722 1229 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.32 % Allowed : 28.95 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.26), residues: 1118 helix: 1.87 (0.27), residues: 384 sheet: 0.02 (0.30), residues: 285 loop : -1.09 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 148 TYR 0.016 0.001 TYR S 178 PHE 0.020 0.001 PHE A 38 TRP 0.011 0.001 TRP S 47 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9038) covalent geometry : angle 0.59168 (12242) SS BOND : bond 0.00360 ( 5) SS BOND : angle 0.97597 ( 10) hydrogen bonds : bond 0.03794 ( 444) hydrogen bonds : angle 4.50950 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.319 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7402 (tttt) cc_final: 0.7070 (mtpm) REVERT: A 80 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6947 (mm) REVERT: A 94 LYS cc_start: 0.7032 (pptt) cc_final: 0.6051 (mmmt) REVERT: A 257 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6564 (mp) REVERT: A 258 LEU cc_start: 0.6982 (pp) cc_final: 0.6080 (mm) REVERT: C 209 LYS cc_start: 0.8804 (pttm) cc_final: 0.8318 (ptpp) REVERT: C 309 ASP cc_start: 0.8509 (m-30) cc_final: 0.8261 (m-30) REVERT: C 350 ASP cc_start: 0.8565 (m-30) cc_final: 0.8300 (m-30) REVERT: B 17 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6419 (tt0) REVERT: B 46 ARG cc_start: 0.8541 (mtp-110) cc_final: 0.7962 (mpt180) REVERT: B 268 ASN cc_start: 0.8212 (t0) cc_final: 0.7795 (t0) REVERT: G 21 MET cc_start: 0.7601 (tpp) cc_final: 0.7333 (tpp) REVERT: S 135 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7659 (m) outliers start: 41 outliers final: 21 residues processed: 165 average time/residue: 0.5075 time to fit residues: 89.0991 Evaluate side-chains 159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.098516 restraints weight = 10504.023| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.33 r_work: 0.2967 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9043 Z= 0.255 Angle : 0.672 10.939 12252 Z= 0.340 Chirality : 0.046 0.236 1386 Planarity : 0.004 0.058 1548 Dihedral : 5.373 43.892 1229 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.58 % Allowed : 29.47 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1118 helix: 1.60 (0.27), residues: 391 sheet: -0.05 (0.30), residues: 287 loop : -1.14 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 148 TYR 0.015 0.002 TYR A 284 PHE 0.017 0.002 PHE C 189 TRP 0.014 0.002 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00608 ( 9038) covalent geometry : angle 0.67093 (12242) SS BOND : bond 0.00457 ( 5) SS BOND : angle 1.21006 ( 10) hydrogen bonds : bond 0.04400 ( 444) hydrogen bonds : angle 4.73577 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.232 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7439 (tttt) cc_final: 0.7095 (mtpm) REVERT: A 80 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7091 (mm) REVERT: A 94 LYS cc_start: 0.7175 (pptt) cc_final: 0.6222 (mmmt) REVERT: A 257 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6568 (mp) REVERT: C 209 LYS cc_start: 0.8871 (pttm) cc_final: 0.8384 (ptpp) REVERT: C 309 ASP cc_start: 0.8516 (m-30) cc_final: 0.8022 (m-30) REVERT: C 350 ASP cc_start: 0.8559 (m-30) cc_final: 0.8325 (m-30) REVERT: B 17 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6426 (tt0) REVERT: B 46 ARG cc_start: 0.8554 (mtp-110) cc_final: 0.7955 (mpt180) REVERT: B 268 ASN cc_start: 0.8187 (t0) cc_final: 0.7758 (t0) REVERT: G 21 MET cc_start: 0.7601 (tpp) cc_final: 0.7333 (tpp) REVERT: S 135 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7626 (m) outliers start: 34 outliers final: 23 residues processed: 149 average time/residue: 0.5532 time to fit residues: 87.2416 Evaluate side-chains 153 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 7 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN B 32 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101111 restraints weight = 10491.696| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.33 r_work: 0.3007 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9043 Z= 0.160 Angle : 0.621 10.105 12252 Z= 0.313 Chirality : 0.044 0.209 1386 Planarity : 0.004 0.045 1548 Dihedral : 5.156 42.598 1229 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.84 % Allowed : 30.11 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.26), residues: 1118 helix: 1.80 (0.27), residues: 380 sheet: -0.06 (0.30), residues: 287 loop : -1.03 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 148 TYR 0.024 0.001 TYR A 269 PHE 0.015 0.001 PHE C 189 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9038) covalent geometry : angle 0.62105 (12242) SS BOND : bond 0.00429 ( 5) SS BOND : angle 1.02874 ( 10) hydrogen bonds : bond 0.03935 ( 444) hydrogen bonds : angle 4.57944 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.354 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. REVERT: A 28 LYS cc_start: 0.7440 (tttt) cc_final: 0.7101 (mtpm) REVERT: A 80 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7062 (mm) REVERT: A 94 LYS cc_start: 0.7099 (pptt) cc_final: 0.6161 (mmmt) REVERT: A 257 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6561 (mp) REVERT: A 258 LEU cc_start: 0.6965 (pp) cc_final: 0.6043 (mm) REVERT: C 209 LYS cc_start: 0.8814 (pttm) cc_final: 0.8325 (ptpp) REVERT: C 309 ASP cc_start: 0.8506 (m-30) cc_final: 0.8247 (m-30) REVERT: C 350 ASP cc_start: 0.8580 (m-30) cc_final: 0.8307 (m-30) REVERT: B 17 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6424 (tt0) REVERT: B 46 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.7965 (mpt180) REVERT: B 268 ASN cc_start: 0.8165 (t0) cc_final: 0.7738 (t0) REVERT: G 21 MET cc_start: 0.7659 (tpp) cc_final: 0.7393 (tpp) REVERT: S 135 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7634 (m) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.5415 time to fit residues: 82.2324 Evaluate side-chains 151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 185 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 269 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099642 restraints weight = 10374.870| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.32 r_work: 0.2986 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9043 Z= 0.216 Angle : 0.647 9.895 12252 Z= 0.326 Chirality : 0.045 0.210 1386 Planarity : 0.004 0.047 1548 Dihedral : 5.194 42.903 1229 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.84 % Allowed : 30.11 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.26), residues: 1118 helix: 1.77 (0.27), residues: 380 sheet: -0.06 (0.30), residues: 287 loop : -1.05 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 148 TYR 0.023 0.002 TYR A 269 PHE 0.019 0.002 PHE A 38 TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 9038) covalent geometry : angle 0.64625 (12242) SS BOND : bond 0.00467 ( 5) SS BOND : angle 1.13400 ( 10) hydrogen bonds : bond 0.04177 ( 444) hydrogen bonds : angle 4.64313 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3557.59 seconds wall clock time: 61 minutes 13.34 seconds (3673.34 seconds total)