Starting phenix.real_space_refine on Thu Jul 2 03:49:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7e1e_30939/07_2026/7e1e_30939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1e_30939/07_2026/7e1e_30939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7e1e_30939/07_2026/7e1e_30939.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7e1e_30939/07_2026/7e1e_30939.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e1e_30939/07_2026/7e1e_30939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1e_30939/07_2026/7e1e_30939.map" model { file = "/net/cci-nas-00/data/ceres_data/7e1e_30939/07_2026/7e1e_30939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1e_30939/07_2026/7e1e_30939.cif" } resolution = 3.34 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 36 5.16 5 C 4128 2.51 5 N 1092 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6489 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "B" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "C" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2161 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 265} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.87, per 1000 atoms: 0.29 Number of scatterers: 6489 At special positions: 0 Unit cell: (91.4578, 87.5382, 78.3924, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 36 16.00 O 1227 8.00 N 1092 7.00 C 4128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 85 " distance=2.02 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 85 " distance=2.02 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 299 " distance=2.02 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 278 " distance=2.04 Simple disulfide: pdb=" SG CYS B 242 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 85 " distance=2.02 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 299 " distance=2.02 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 278 " distance=2.04 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 245 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 284 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 450.2 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1506 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 24.7% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 4.141A pdb=" N GLY A 91 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 242 through 247 removed outlier: 4.019A pdb=" N LEU A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 247' Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.837A pdb=" N HIS A 282 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'B' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 4.142A pdb=" N GLY B 91 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 247 removed outlier: 4.018A pdb=" N LEU B 246 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 242 through 247' Processing helix chain 'B' and resid 279 through 283 removed outlier: 3.836A pdb=" N HIS B 282 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.823A pdb=" N ILE C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 4.141A pdb=" N GLY C 91 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 157 Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.020A pdb=" N LEU C 246 " --> pdb=" O CYS C 242 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 247' Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.836A pdb=" N HIS C 282 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 74 removed outlier: 25.097A pdb=" N PHE A 80 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL A 100 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN A 82 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA A 98 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 25.097A pdb=" N PHE A 80 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL A 100 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN A 82 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA A 98 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 329 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A 99 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 327 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE A 164 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 184 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG A 185 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA A 267 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 259 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 249 through 251 Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE B 80 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL B 100 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN B 82 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA B 98 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE B 80 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL B 100 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 13.344A pdb=" N GLN B 82 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA B 98 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE B 329 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER B 99 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 327 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE B 164 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 184 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG B 185 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 267 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 259 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 249 through 251 Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE C 80 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL C 100 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 13.345A pdb=" N GLN C 82 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA C 98 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 69 through 74 removed outlier: 25.098A pdb=" N PHE C 80 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 19.942A pdb=" N VAL C 100 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 13.345A pdb=" N GLN C 82 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ALA C 98 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE C 329 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER C 99 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL C 327 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE C 164 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 184 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ARG C 185 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 267 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE C 259 " --> pdb=" O PRO C 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 249 through 251 201 hydrogen bonds defined for protein. 486 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: 1.12 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2106 1.34 - 1.47: 1823 1.47 - 1.59: 2701 1.59 - 1.71: 0 1.71 - 1.83: 39 Bond restraints: 6669 Sorted by residual: bond pdb=" CB PHE C 184 " pdb=" CG PHE C 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.96e+00 bond pdb=" CB PHE A 184 " pdb=" CG PHE A 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.92e+00 bond pdb=" CB PHE B 184 " pdb=" CG PHE B 184 " ideal model delta sigma weight residual 1.502 1.470 0.032 2.30e-02 1.89e+03 1.90e+00 bond pdb=" C TYR C 208 " pdb=" O TYR C 208 " ideal model delta sigma weight residual 1.240 1.223 0.017 1.24e-02 6.50e+03 1.78e+00 bond pdb=" C TYR A 208 " pdb=" O TYR A 208 " ideal model delta sigma weight residual 1.240 1.223 0.016 1.24e-02 6.50e+03 1.76e+00 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 8489 1.61 - 3.22: 507 3.22 - 4.84: 70 4.84 - 6.45: 15 6.45 - 8.06: 3 Bond angle restraints: 9084 Sorted by residual: angle pdb=" CA CYS C 242 " pdb=" CB CYS C 242 " pdb=" SG CYS C 242 " ideal model delta sigma weight residual 114.40 122.46 -8.06 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS B 242 " pdb=" CB CYS B 242 " pdb=" SG CYS B 242 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS A 242 " pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CB GLN B 177 " pdb=" CG GLN B 177 " pdb=" CD GLN B 177 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.70e+00 3.46e-01 1.08e+01 angle pdb=" CB GLN C 177 " pdb=" CG GLN C 177 " pdb=" CD GLN C 177 " ideal model delta sigma weight residual 112.60 118.18 -5.58 1.70e+00 3.46e-01 1.08e+01 ... (remaining 9079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 3573 25.96 - 51.93: 234 51.93 - 77.89: 42 77.89 - 103.85: 6 103.85 - 129.82: 3 Dihedral angle restraints: 3858 sinusoidal: 1476 harmonic: 2382 Sorted by residual: dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N TYR C 208 " pdb=" CA TYR C 208 " ideal model delta harmonic sigma weight residual 180.00 50.18 129.82 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N TYR A 208 " pdb=" CA TYR A 208 " ideal model delta harmonic sigma weight residual 180.00 50.20 129.80 0 5.00e+00 4.00e-02 6.74e+02 dihedral pdb=" CA PHE B 207 " pdb=" C PHE B 207 " pdb=" N TYR B 208 " pdb=" CA TYR B 208 " ideal model delta harmonic sigma weight residual 180.00 50.24 129.76 0 5.00e+00 4.00e-02 6.73e+02 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 543 0.037 - 0.074: 278 0.074 - 0.111: 118 0.111 - 0.148: 12 0.148 - 0.185: 6 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA VAL C 258 " pdb=" N VAL C 258 " pdb=" C VAL C 258 " pdb=" CB VAL C 258 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA VAL B 258 " pdb=" N VAL B 258 " pdb=" C VAL B 258 " pdb=" CB VAL B 258 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA VAL A 258 " pdb=" N VAL A 258 " pdb=" C VAL A 258 " pdb=" CB VAL A 258 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 954 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 217 " 0.063 5.00e-02 4.00e+02 9.51e-02 1.45e+01 pdb=" N PRO A 218 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 217 " -0.063 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO B 218 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 217 " 0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO C 218 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO C 218 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 218 " 0.051 5.00e-02 4.00e+02 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 385 2.70 - 3.25: 6803 3.25 - 3.80: 11014 3.80 - 4.35: 14816 4.35 - 4.90: 24438 Nonbonded interactions: 57456 Sorted by model distance: nonbonded pdb=" O LYS C 62 " pdb=" NZ LYS C 64 " model vdw 2.154 3.120 nonbonded pdb=" O LYS A 62 " pdb=" NZ LYS A 64 " model vdw 2.155 3.120 nonbonded pdb=" O LYS B 62 " pdb=" NZ LYS B 64 " model vdw 2.155 3.120 nonbonded pdb=" OG SER A 77 " pdb=" OE2 GLU B 144 " model vdw 2.159 3.040 nonbonded pdb=" OD1 ASP B 149 " pdb=" N ASP B 150 " model vdw 2.187 3.120 ... (remaining 57451 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.850 Find NCS groups from input model: 0.070 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 6684 Z= 0.337 Angle : 0.865 8.062 9114 Z= 0.504 Chirality : 0.050 0.185 957 Planarity : 0.007 0.095 1188 Dihedral : 17.656 129.817 2307 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.03 % Favored : 90.61 % Rotamer: Outliers : 11.79 % Allowed : 5.82 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 15.38 % Twisted General : 0.38 % 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 are not related in a simple way. whole: -3.79 (0.23), residues: 831 helix: -3.33 (0.39), residues: 96 sheet: -1.21 (0.48), residues: 96 loop : -2.85 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 257 TYR 0.012 0.002 TYR C 201 PHE 0.015 0.002 PHE C 127 TRP 0.005 0.001 TRP C 178 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.34 ( 6669) covalent geometry : angle 0.85788 / 0.50 ( 9084) SS BOND : bond 0.00771 / 0.46 ( 15) SS BOND : angle 2.07754 / 1.47 ( 30) hydrogen bonds : bond 0.19877 / 13.02 ( 174) hydrogen bonds : angle 8.13608 / 5.53 ( 486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 171 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8410 (m-40) cc_final: 0.8200 (m110) REVERT: A 305 PHE cc_start: 0.8203 (m-10) cc_final: 0.7900 (m-10) REVERT: B 202 PHE cc_start: 0.7975 (m-80) cc_final: 0.7761 (m-10) REVERT: B 307 TRP cc_start: 0.6919 (t-100) cc_final: 0.6679 (t-100) REVERT: B 321 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8808 (t) REVERT: C 314 VAL cc_start: 0.6846 (OUTLIER) cc_final: 0.6635 (m) REVERT: C 320 LYS cc_start: 0.8542 (tttm) cc_final: 0.8329 (ttmm) outliers start: 81 outliers final: 13 residues processed: 227 average time/residue: 0.0889 time to fit residues: 26.1535 Evaluate side-chains 118 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 282 HIS B 240 GLN B 277 ASN B 282 HIS C 122 ASN C 240 GLN ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.117103 restraints weight = 9801.331| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.85 r_work: 0.3353 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6684 Z= 0.160 Angle : 0.720 8.524 9114 Z= 0.381 Chirality : 0.048 0.223 957 Planarity : 0.006 0.074 1188 Dihedral : 9.777 90.731 937 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.66 % Favored : 93.98 % Rotamer: Outliers : 4.95 % Allowed : 13.54 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % 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 are not related in a simple way. whole: -3.03 (0.26), residues: 831 helix: -3.08 (0.39), residues: 117 sheet: -0.85 (0.49), residues: 90 loop : -2.14 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 257 TYR 0.030 0.002 TYR A 208 PHE 0.012 0.001 PHE A 80 TRP 0.011 0.001 TRP C 94 HIS 0.009 0.002 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 6669) covalent geometry : angle 0.71244 / 0.38 ( 9084) SS BOND : bond 0.00513 / 0.33 ( 15) SS BOND : angle 1.90134 / 1.33 ( 30) hydrogen bonds : bond 0.03409 / 2.24 ( 174) hydrogen bonds : angle 6.05719 / 4.14 ( 486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8403 (ptmm) REVERT: A 293 GLU cc_start: 0.6878 (tt0) cc_final: 0.6314 (tt0) REVERT: B 79 GLN cc_start: 0.8956 (tt0) cc_final: 0.8613 (tt0) REVERT: B 142 ARG cc_start: 0.7163 (mtt90) cc_final: 0.6660 (mpt180) REVERT: B 158 ASP cc_start: 0.7430 (t0) cc_final: 0.6685 (t0) REVERT: B 212 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8683 (t80) REVERT: B 293 GLU cc_start: 0.8048 (tt0) cc_final: 0.7821 (tt0) REVERT: B 307 TRP cc_start: 0.7364 (t-100) cc_final: 0.7060 (t-100) REVERT: B 310 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8412 (mt) REVERT: C 163 ASP cc_start: 0.6970 (m-30) cc_final: 0.6753 (m-30) REVERT: C 202 PHE cc_start: 0.8425 (m-80) cc_final: 0.8200 (m-80) REVERT: C 231 PHE cc_start: 0.8369 (t80) cc_final: 0.8032 (t80) REVERT: C 301 ASP cc_start: 0.9142 (m-30) cc_final: 0.8938 (m-30) outliers start: 34 outliers final: 16 residues processed: 147 average time/residue: 0.0865 time to fit residues: 16.6222 Evaluate side-chains 121 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109085 restraints weight = 9753.066| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.84 r_work: 0.3233 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6684 Z= 0.194 Angle : 0.685 7.063 9114 Z= 0.367 Chirality : 0.049 0.200 957 Planarity : 0.006 0.079 1188 Dihedral : 8.782 58.570 922 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 5.24 % Allowed : 15.28 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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 are not related in a simple way. whole: -2.78 (0.27), residues: 831 helix: -2.88 (0.40), residues: 117 sheet: -0.42 (0.44), residues: 120 loop : -2.08 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 257 TYR 0.017 0.002 TYR A 208 PHE 0.014 0.002 PHE B 330 TRP 0.014 0.001 TRP C 94 HIS 0.007 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 6669) covalent geometry : angle 0.68004 / 0.37 ( 9084) SS BOND : bond 0.00580 / 0.36 ( 15) SS BOND : angle 1.54249 / 1.04 ( 30) hydrogen bonds : bond 0.03809 / 2.47 ( 174) hydrogen bonds : angle 6.13172 / 4.20 ( 486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 CYS cc_start: 0.6970 (m) cc_final: 0.6756 (m) REVERT: A 272 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8491 (pp) REVERT: A 293 GLU cc_start: 0.7225 (tt0) cc_final: 0.6700 (tt0) REVERT: C 202 PHE cc_start: 0.8489 (m-80) cc_final: 0.8215 (m-80) REVERT: C 205 LYS cc_start: 0.7296 (mmtp) cc_final: 0.7059 (mmtp) REVERT: C 208 TYR cc_start: 0.5944 (t80) cc_final: 0.5349 (t80) REVERT: C 231 PHE cc_start: 0.8540 (t80) cc_final: 0.8306 (t80) REVERT: C 261 ASN cc_start: 0.7958 (m-40) cc_final: 0.7619 (m-40) outliers start: 36 outliers final: 21 residues processed: 133 average time/residue: 0.1045 time to fit residues: 17.6749 Evaluate side-chains 116 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 293 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN B 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104699 restraints weight = 10045.144| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.81 r_work: 0.3167 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 6684 Z= 0.239 Angle : 0.736 9.040 9114 Z= 0.389 Chirality : 0.051 0.188 957 Planarity : 0.006 0.081 1188 Dihedral : 8.591 54.043 920 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.03 % Favored : 90.85 % Rotamer: Outliers : 5.82 % Allowed : 14.85 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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 are not related in a simple way. whole: -2.51 (0.27), residues: 831 helix: -2.46 (0.42), residues: 117 sheet: -0.40 (0.44), residues: 120 loop : -1.90 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 257 TYR 0.017 0.002 TYR B 151 PHE 0.016 0.002 PHE B 330 TRP 0.017 0.001 TRP A 307 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 ( 6669) covalent geometry : angle 0.73243 / 0.39 ( 9084) SS BOND : bond 0.00531 / 0.37 ( 15) SS BOND : angle 1.47985 / 1.00 ( 30) hydrogen bonds : bond 0.03964 / 2.55 ( 174) hydrogen bonds : angle 6.32782 / 4.37 ( 486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8206 (p0) cc_final: 0.7747 (p0) REVERT: A 162 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 272 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8657 (pp) REVERT: A 293 GLU cc_start: 0.7304 (tt0) cc_final: 0.6994 (tt0) REVERT: B 73 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8411 (mt) REVERT: B 310 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8460 (mt) REVERT: C 87 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8074 (mtm) REVERT: C 202 PHE cc_start: 0.8481 (m-80) cc_final: 0.8215 (m-80) REVERT: C 208 TYR cc_start: 0.5979 (t80) cc_final: 0.5384 (t80) REVERT: C 261 ASN cc_start: 0.8626 (m-40) cc_final: 0.8417 (m-40) REVERT: C 275 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7535 (mt) outliers start: 40 outliers final: 22 residues processed: 130 average time/residue: 0.1003 time to fit residues: 16.0480 Evaluate side-chains 116 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105038 restraints weight = 9976.092| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.84 r_work: 0.3175 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6684 Z= 0.195 Angle : 0.714 9.345 9114 Z= 0.378 Chirality : 0.050 0.195 957 Planarity : 0.006 0.080 1188 Dihedral : 8.204 52.643 916 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.82 % Favored : 92.06 % Rotamer: Outliers : 4.80 % Allowed : 16.45 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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 are not related in a simple way. whole: -2.39 (0.28), residues: 831 helix: -2.60 (0.40), residues: 117 sheet: -0.32 (0.45), residues: 120 loop : -1.76 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 257 TYR 0.014 0.002 TYR B 212 PHE 0.014 0.001 PHE A 330 TRP 0.010 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 6669) covalent geometry : angle 0.70327 / 0.37 ( 9084) SS BOND : bond 0.00542 / 0.40 ( 15) SS BOND : angle 2.22692 / 1.48 ( 30) hydrogen bonds : bond 0.03729 / 2.40 ( 174) hydrogen bonds : angle 6.07126 / 4.23 ( 486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7030 (mm-30) REVERT: A 177 GLN cc_start: 0.8677 (mp10) cc_final: 0.8451 (mt0) REVERT: A 272 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8702 (pp) REVERT: A 293 GLU cc_start: 0.7282 (tt0) cc_final: 0.6957 (tt0) REVERT: B 73 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8352 (mt) REVERT: B 307 TRP cc_start: 0.7724 (t-100) cc_final: 0.7498 (t-100) REVERT: B 310 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8449 (mt) REVERT: C 87 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7862 (mpp) REVERT: C 202 PHE cc_start: 0.8485 (m-80) cc_final: 0.8223 (m-80) REVERT: C 208 TYR cc_start: 0.5741 (t80) cc_final: 0.5313 (t80) REVERT: C 261 ASN cc_start: 0.8740 (m-40) cc_final: 0.8524 (m-40) outliers start: 33 outliers final: 22 residues processed: 123 average time/residue: 0.0950 time to fit residues: 14.7507 Evaluate side-chains 117 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 66 optimal weight: 0.0870 chunk 33 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104965 restraints weight = 10066.288| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.80 r_work: 0.3176 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 6684 Z= 0.208 Angle : 0.750 12.889 9114 Z= 0.394 Chirality : 0.049 0.194 957 Planarity : 0.007 0.080 1188 Dihedral : 8.095 53.088 914 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.03 % Favored : 90.61 % Rotamer: Outliers : 5.09 % Allowed : 16.30 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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 are not related in a simple way. whole: -2.43 (0.28), residues: 831 helix: -2.65 (0.40), residues: 117 sheet: -0.55 (0.53), residues: 87 loop : -1.69 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 257 TYR 0.013 0.002 TYR B 212 PHE 0.015 0.001 PHE B 330 TRP 0.010 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 6669) covalent geometry : angle 0.73752 / 0.39 ( 9084) SS BOND : bond 0.00518 / 0.39 ( 15) SS BOND : angle 2.47881 / 1.57 ( 30) hydrogen bonds : bond 0.03773 / 2.42 ( 174) hydrogen bonds : angle 6.03343 / 4.18 ( 486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8276 (p0) cc_final: 0.8030 (p0) REVERT: A 177 GLN cc_start: 0.8751 (mp10) cc_final: 0.8527 (mt0) REVERT: A 293 GLU cc_start: 0.7320 (tt0) cc_final: 0.7024 (tt0) REVERT: B 73 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8356 (mt) REVERT: B 310 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8417 (mt) REVERT: C 87 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7880 (mpp) REVERT: C 202 PHE cc_start: 0.8527 (m-80) cc_final: 0.8269 (m-80) REVERT: C 208 TYR cc_start: 0.5755 (t80) cc_final: 0.5311 (t80) REVERT: C 275 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8098 (mt) outliers start: 35 outliers final: 25 residues processed: 121 average time/residue: 0.0862 time to fit residues: 13.2128 Evaluate side-chains 121 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.123179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105725 restraints weight = 9958.061| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.80 r_work: 0.3188 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6684 Z= 0.177 Angle : 0.718 10.274 9114 Z= 0.381 Chirality : 0.049 0.196 957 Planarity : 0.006 0.078 1188 Dihedral : 8.025 53.553 914 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.73 % Rotamer: Outliers : 4.80 % Allowed : 17.61 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.88 % 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 are not related in a simple way. whole: -2.33 (0.28), residues: 831 helix: -2.60 (0.42), residues: 99 sheet: -0.54 (0.53), residues: 87 loop : -1.64 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 257 TYR 0.013 0.002 TYR A 253 PHE 0.016 0.001 PHE B 184 TRP 0.007 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 6669) covalent geometry : angle 0.70669 / 0.38 ( 9084) SS BOND : bond 0.00386 / 0.27 ( 15) SS BOND : angle 2.31062 / 1.46 ( 30) hydrogen bonds : bond 0.03596 / 2.28 ( 174) hydrogen bonds : angle 5.86696 / 4.07 ( 486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8161 (p0) cc_final: 0.7931 (p0) REVERT: A 132 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7711 (mtm-85) REVERT: A 163 ASP cc_start: 0.8136 (m-30) cc_final: 0.7926 (m-30) REVERT: A 177 GLN cc_start: 0.8722 (mp10) cc_final: 0.8298 (mt0) REVERT: A 293 GLU cc_start: 0.7205 (tt0) cc_final: 0.6848 (tt0) REVERT: B 73 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8349 (mt) REVERT: B 310 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8407 (mt) REVERT: C 87 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: C 202 PHE cc_start: 0.8489 (m-80) cc_final: 0.8287 (m-80) REVERT: C 275 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8128 (mt) outliers start: 33 outliers final: 27 residues processed: 123 average time/residue: 0.0914 time to fit residues: 14.0417 Evaluate side-chains 128 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.106208 restraints weight = 9999.121| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.80 r_work: 0.3193 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6684 Z= 0.173 Angle : 0.702 7.963 9114 Z= 0.372 Chirality : 0.048 0.195 957 Planarity : 0.007 0.078 1188 Dihedral : 7.890 53.043 914 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.54 % Favored : 91.34 % Rotamer: Outliers : 5.39 % Allowed : 17.47 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.88 % 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 are not related in a simple way. whole: -2.31 (0.28), residues: 831 helix: -2.59 (0.43), residues: 99 sheet: -0.55 (0.53), residues: 87 loop : -1.62 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 257 TYR 0.023 0.002 TYR C 208 PHE 0.022 0.001 PHE B 184 TRP 0.008 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 6669) covalent geometry : angle 0.69394 / 0.37 ( 9084) SS BOND : bond 0.00424 / 0.27 ( 15) SS BOND : angle 2.00769 / 1.18 ( 30) hydrogen bonds : bond 0.03562 / 2.25 ( 174) hydrogen bonds : angle 5.78710 / 4.00 ( 486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8135 (p0) cc_final: 0.7888 (p0) REVERT: A 132 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7646 (mtm-85) REVERT: A 245 CYS cc_start: 0.7751 (m) cc_final: 0.7487 (m) REVERT: A 257 ARG cc_start: 0.8238 (ttt-90) cc_final: 0.7889 (tmt-80) REVERT: A 293 GLU cc_start: 0.7254 (tt0) cc_final: 0.6885 (tt0) REVERT: B 73 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8343 (mt) REVERT: B 310 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8421 (mt) REVERT: C 87 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7841 (mpp) REVERT: C 275 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8145 (mt) outliers start: 37 outliers final: 27 residues processed: 124 average time/residue: 0.0892 time to fit residues: 13.9952 Evaluate side-chains 120 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 30 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105866 restraints weight = 10168.500| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.81 r_work: 0.3190 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6684 Z= 0.186 Angle : 0.733 9.957 9114 Z= 0.388 Chirality : 0.049 0.218 957 Planarity : 0.007 0.077 1188 Dihedral : 7.854 54.182 914 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.27 % Favored : 90.61 % Rotamer: Outliers : 4.37 % Allowed : 19.36 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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 are not related in a simple way. whole: -2.31 (0.28), residues: 831 helix: -2.59 (0.43), residues: 99 sheet: -0.56 (0.54), residues: 87 loop : -1.62 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 257 TYR 0.024 0.002 TYR B 208 PHE 0.014 0.001 PHE B 330 TRP 0.008 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 6669) covalent geometry : angle 0.72529 / 0.39 ( 9084) SS BOND : bond 0.00428 / 0.28 ( 15) SS BOND : angle 1.97138 / 1.14 ( 30) hydrogen bonds : bond 0.03672 / 2.31 ( 174) hydrogen bonds : angle 5.79695 / 4.01 ( 486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7196 (tt0) cc_final: 0.6871 (tt0) REVERT: B 73 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8364 (mt) REVERT: B 310 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8437 (mt) REVERT: C 87 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7849 (mpp) REVERT: C 257 ARG cc_start: 0.7375 (tmt170) cc_final: 0.6893 (ttm-80) REVERT: C 275 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8270 (mt) outliers start: 30 outliers final: 26 residues processed: 114 average time/residue: 0.1041 time to fit residues: 14.8899 Evaluate side-chains 124 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104520 restraints weight = 10085.454| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.77 r_work: 0.3170 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6684 Z= 0.216 Angle : 0.759 10.107 9114 Z= 0.401 Chirality : 0.050 0.204 957 Planarity : 0.007 0.080 1188 Dihedral : 7.929 54.696 914 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.73 % Rotamer: Outliers : 4.51 % Allowed : 19.36 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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 are not related in a simple way. whole: -2.39 (0.28), residues: 831 helix: -2.65 (0.43), residues: 99 sheet: -0.58 (0.54), residues: 87 loop : -1.69 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 257 TYR 0.028 0.002 TYR B 208 PHE 0.024 0.002 PHE B 184 TRP 0.010 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 ( 6669) covalent geometry : angle 0.75047 / 0.40 ( 9084) SS BOND : bond 0.00421 / 0.29 ( 15) SS BOND : angle 2.10356 / 1.21 ( 30) hydrogen bonds : bond 0.03889 / 2.47 ( 174) hydrogen bonds : angle 5.95469 / 4.11 ( 486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8165 (p0) cc_final: 0.7724 (p0) REVERT: A 293 GLU cc_start: 0.7203 (tt0) cc_final: 0.6941 (tt0) REVERT: B 73 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8430 (mt) REVERT: C 87 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: C 202 PHE cc_start: 0.8606 (m-80) cc_final: 0.8315 (m-80) REVERT: C 257 ARG cc_start: 0.6942 (tmt170) cc_final: 0.6401 (ttm-80) REVERT: C 275 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8284 (mt) outliers start: 31 outliers final: 28 residues processed: 113 average time/residue: 0.0947 time to fit residues: 13.5042 Evaluate side-chains 122 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 255 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 72 CYS Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 114 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106106 restraints weight = 9987.521| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.79 r_work: 0.3191 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6684 Z= 0.175 Angle : 0.721 9.286 9114 Z= 0.382 Chirality : 0.048 0.214 957 Planarity : 0.007 0.077 1188 Dihedral : 7.757 53.827 914 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.18 % Favored : 91.70 % Rotamer: Outliers : 4.66 % Allowed : 19.51 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % 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 are not related in a simple way. whole: -2.42 (0.28), residues: 831 helix: -2.53 (0.44), residues: 96 sheet: -0.54 (0.54), residues: 87 loop : -1.76 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 132 TYR 0.025 0.002 TYR C 208 PHE 0.013 0.001 PHE B 330 TRP 0.008 0.001 TRP A 307 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 ( 6669) covalent geometry : angle 0.71489 / 0.38 ( 9084) SS BOND : bond 0.00400 / 0.26 ( 15) SS BOND : angle 1.74566 / 1.01 ( 30) hydrogen bonds : bond 0.03587 / 2.27 ( 174) hydrogen bonds : angle 5.74397 / 3.96 ( 486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1473.10 seconds wall clock time: 25 minutes 55.77 seconds (1555.77 seconds total)