Starting phenix.real_space_refine on Tue Mar 3 15:05:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e1e_30939/03_2026/7e1e_30939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1e_30939/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7e1e_30939/03_2026/7e1e_30939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1e_30939/03_2026/7e1e_30939.map" model { file = "/net/cci-nas-00/data/ceres_data/7e1e_30939/03_2026/7e1e_30939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1e_30939/03_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-5986/lib/python3.9/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: 1.98, per 1000 atoms: 0.31 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: 0.76 Conformation dependent library (CDL) restraints added in 226.6 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: 0.27 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: 1.06 Time building geometry restraints manager: 0.96 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: 0.01 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: 1.650 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 covalent geometry : bond 0.00728 ( 6669) covalent geometry : angle 0.85788 ( 9084) SS BOND : bond 0.00771 ( 15) SS BOND : angle 2.07754 ( 30) hydrogen bonds : bond 0.19877 ( 174) hydrogen bonds : angle 8.13608 ( 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 : 0.244 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: 0.0980 time to fit residues: 28.4002 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 : 0.251 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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: 0.8022 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 covalent geometry : bond 0.00377 ( 6669) covalent geometry : angle 0.71244 ( 9084) SS BOND : bond 0.00513 ( 15) SS BOND : angle 1.90134 ( 30) hydrogen bonds : bond 0.03409 ( 174) hydrogen bonds : angle 6.05719 ( 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 : 0.234 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: 0.6661 (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 307 TRP cc_start: 0.7364 (t-100) cc_final: 0.7063 (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: 0.8033 (t80) REVERT: C 301 ASP cc_start: 0.9142 (m-30) cc_final: 0.8937 (m-30) outliers start: 34 outliers final: 16 residues processed: 147 average time/residue: 0.0946 time to fit residues: 17.9715 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 : 0.198 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.126695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109116 restraints weight = 9748.801| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.84 r_work: 0.3232 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4072 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= 0.196 Angle : 0.687 6.865 9114 Z= 0.368 Chirality : 0.049 0.200 957 Planarity : 0.006 0.079 1188 Dihedral : 8.783 58.552 922 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 5.09 % Allowed : 15.43 % 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: -2.56 (0.27), residues: 831 helix: -2.46 (0.46), residues: 99 sheet: -0.42 (0.44), residues: 120 loop : -1.99 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 257 TYR 0.015 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 covalent geometry : bond 0.00453 ( 6669) covalent geometry : angle 0.68210 ( 9084) SS BOND : bond 0.00522 ( 15) SS BOND : angle 1.56733 ( 30) hydrogen bonds : bond 0.03798 ( 174) hydrogen bonds : angle 6.12019 ( 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 145 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 CYS cc_start: 0.6971 (m) cc_final: 0.6751 (m) REVERT: A 272 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8502 (pp) REVERT: A 293 GLU cc_start: 0.7090 (tt0) cc_final: 0.6594 (tt0) REVERT: C 202 PHE cc_start: 0.8489 (m-80) cc_final: 0.8211 (m-80) REVERT: C 205 LYS cc_start: 0.7292 (mmtp) cc_final: 0.7045 (mmtp) REVERT: C 208 TYR cc_start: 0.5943 (t80) cc_final: 0.5329 (t80) REVERT: C 231 PHE cc_start: 0.8537 (t80) cc_final: 0.8303 (t80) REVERT: C 261 ASN cc_start: 0.7952 (m-40) cc_final: 0.7605 (m-40) outliers start: 35 outliers final: 21 residues processed: 132 average time/residue: 0.1112 time to fit residues: 18.4022 Evaluate side-chains 118 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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: 8.9990 chunk 54 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN B 79 GLN C 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.104747 restraints weight = 10027.346| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.81 r_work: 0.3170 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 6684 Z= 0.239 Angle : 0.727 7.365 9114 Z= 0.386 Chirality : 0.050 0.188 957 Planarity : 0.006 0.081 1188 Dihedral : 8.585 54.252 920 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.73 % Rotamer: Outliers : 5.97 % Allowed : 14.56 % 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: -2.51 (0.27), residues: 831 helix: -2.45 (0.42), residues: 117 sheet: -0.38 (0.44), residues: 120 loop : -1.91 (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 A 330 TRP 0.017 0.001 TRP A 307 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 6669) covalent geometry : angle 0.72245 ( 9084) SS BOND : bond 0.00524 ( 15) SS BOND : angle 1.52500 ( 30) hydrogen bonds : bond 0.03960 ( 174) hydrogen bonds : angle 6.30351 ( 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: 41 poor density : 102 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8180 (p0) cc_final: 0.7709 (p0) REVERT: A 272 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8647 (pp) REVERT: A 293 GLU cc_start: 0.7307 (tt0) cc_final: 0.7010 (tt0) REVERT: B 73 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 310 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8453 (mt) REVERT: C 87 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8059 (mtm) REVERT: C 202 PHE cc_start: 0.8501 (m-80) cc_final: 0.8238 (m-80) REVERT: C 208 TYR cc_start: 0.5998 (t80) cc_final: 0.5434 (t80) REVERT: C 261 ASN cc_start: 0.8610 (m-40) cc_final: 0.8408 (m-40) outliers start: 41 outliers final: 24 residues processed: 131 average time/residue: 0.1119 time to fit residues: 18.1306 Evaluate side-chains 117 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 77 SER 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 280 THR 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 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: 2.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.121392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103851 restraints weight = 10025.115| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.79 r_work: 0.3157 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6684 Z= 0.246 Angle : 0.744 9.587 9114 Z= 0.396 Chirality : 0.051 0.189 957 Planarity : 0.007 0.083 1188 Dihedral : 8.416 56.294 916 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.15 % Favored : 90.73 % Rotamer: Outliers : 5.24 % Allowed : 15.87 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % 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: -2.71 (0.39), residues: 117 sheet: -0.60 (0.52), residues: 87 loop : -1.74 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 257 TYR 0.015 0.002 TYR B 151 PHE 0.017 0.002 PHE B 330 TRP 0.013 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 6669) covalent geometry : angle 0.73564 ( 9084) SS BOND : bond 0.00651 ( 15) SS BOND : angle 2.01921 ( 30) hydrogen bonds : bond 0.04017 ( 174) hydrogen bonds : angle 6.28212 ( 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 133 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8415 (p0) cc_final: 0.7981 (p0) REVERT: A 132 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: A 177 GLN cc_start: 0.8714 (mp10) cc_final: 0.8466 (mt0) REVERT: A 293 GLU cc_start: 0.7162 (tt0) cc_final: 0.6934 (tt0) REVERT: B 73 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 310 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8416 (mt) REVERT: C 87 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7897 (mpp) REVERT: C 202 PHE cc_start: 0.8525 (m-80) cc_final: 0.8285 (m-80) REVERT: C 208 TYR cc_start: 0.5865 (t80) cc_final: 0.5387 (t80) outliers start: 36 outliers final: 25 residues processed: 122 average time/residue: 0.1198 time to fit residues: 18.0337 Evaluate side-chains 124 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 147 THR 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 75 THR Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 89 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 298 GLN 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 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: 5.9990 chunk 33 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106272 restraints weight = 9936.804| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.84 r_work: 0.3195 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 6684 Z= 0.160 Angle : 0.710 12.913 9114 Z= 0.374 Chirality : 0.048 0.202 957 Planarity : 0.006 0.078 1188 Dihedral : 8.031 55.912 914 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.82 % Favored : 91.82 % Rotamer: Outliers : 4.22 % Allowed : 18.20 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % 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: -0.48 (0.53), residues: 87 loop : -1.63 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 132 TYR 0.012 0.002 TYR A 253 PHE 0.011 0.001 PHE B 330 TRP 0.006 0.001 TRP A 307 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6669) covalent geometry : angle 0.69509 ( 9084) SS BOND : bond 0.00425 ( 15) SS BOND : angle 2.60028 ( 30) hydrogen bonds : bond 0.03515 ( 174) hydrogen bonds : angle 5.86480 ( 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 138 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8150 (mp0) cc_final: 0.7836 (mp0) REVERT: A 129 ASP cc_start: 0.8378 (p0) cc_final: 0.7971 (p0) REVERT: A 132 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7862 (mtm-85) REVERT: A 163 ASP cc_start: 0.8211 (m-30) cc_final: 0.7963 (m-30) REVERT: A 177 GLN cc_start: 0.8717 (mp10) cc_final: 0.8495 (mt0) REVERT: A 257 ARG cc_start: 0.8243 (tmt170) cc_final: 0.7977 (tmt-80) REVERT: A 293 GLU cc_start: 0.7234 (tt0) cc_final: 0.6949 (tt0) REVERT: B 73 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8302 (mt) REVERT: B 310 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8414 (mt) REVERT: C 87 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7866 (mpp) REVERT: C 202 PHE cc_start: 0.8500 (m-80) cc_final: 0.8241 (m-80) REVERT: C 208 TYR cc_start: 0.5612 (t80) cc_final: 0.5191 (t80) REVERT: C 275 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7949 (mt) outliers start: 29 outliers final: 20 residues processed: 128 average time/residue: 0.1068 time to fit residues: 17.0767 Evaluate side-chains 118 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 228 VAL 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 125 VAL 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 310 ILE 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: 1.9990 chunk 16 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 61 optimal weight: 0.0070 chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN C 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109002 restraints weight = 9822.293| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.83 r_work: 0.3235 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6684 Z= 0.141 Angle : 0.688 9.256 9114 Z= 0.365 Chirality : 0.047 0.203 957 Planarity : 0.006 0.076 1188 Dihedral : 7.830 54.865 914 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.46 % Favored : 92.30 % Rotamer: Outliers : 4.37 % Allowed : 18.20 % Favored : 77.44 % 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: -2.21 (0.28), residues: 831 helix: -2.34 (0.45), residues: 96 sheet: -0.46 (0.54), residues: 87 loop : -1.60 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 132 TYR 0.013 0.001 TYR A 208 PHE 0.024 0.001 PHE B 184 TRP 0.005 0.001 TRP B 307 HIS 0.004 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6669) covalent geometry : angle 0.67856 ( 9084) SS BOND : bond 0.00303 ( 15) SS BOND : angle 2.09331 ( 30) hydrogen bonds : bond 0.03285 ( 174) hydrogen bonds : angle 5.52494 ( 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 130 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8100 (mp0) cc_final: 0.7643 (mp0) REVERT: A 62 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7435 (mmtm) REVERT: A 163 ASP cc_start: 0.8075 (m-30) cc_final: 0.7860 (m-30) REVERT: A 177 GLN cc_start: 0.8801 (mp10) cc_final: 0.8395 (mt0) REVERT: A 257 ARG cc_start: 0.8239 (tmt170) cc_final: 0.8000 (tmt-80) REVERT: A 293 GLU cc_start: 0.7282 (tt0) cc_final: 0.6882 (tt0) REVERT: B 310 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8453 (mt) REVERT: C 87 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7870 (mpp) REVERT: C 207 PHE cc_start: 0.5166 (OUTLIER) cc_final: 0.4627 (p90) REVERT: C 208 TYR cc_start: 0.5299 (t80) cc_final: 0.4969 (t80) REVERT: C 275 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7906 (mt) outliers start: 30 outliers final: 23 residues processed: 119 average time/residue: 0.1249 time to fit residues: 18.2551 Evaluate side-chains 123 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 77 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 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 298 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 329 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 125 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 240 GLN Chi-restraints excluded: chain C residue 275 LEU 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: 7.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.121397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103895 restraints weight = 10082.467| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.81 r_work: 0.3158 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 6684 Z= 0.252 Angle : 0.757 8.103 9114 Z= 0.403 Chirality : 0.051 0.190 957 Planarity : 0.007 0.081 1188 Dihedral : 8.126 55.631 914 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.27 % Favored : 90.49 % Rotamer: Outliers : 5.53 % Allowed : 17.90 % Favored : 76.56 % 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: -2.38 (0.27), residues: 831 helix: -2.66 (0.43), residues: 99 sheet: -0.65 (0.54), residues: 87 loop : -1.67 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 257 TYR 0.015 0.002 TYR B 212 PHE 0.022 0.002 PHE C 184 TRP 0.013 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 6669) covalent geometry : angle 0.74866 ( 9084) SS BOND : bond 0.00577 ( 15) SS BOND : angle 2.09927 ( 30) hydrogen bonds : bond 0.04030 ( 174) hydrogen bonds : angle 6.08419 ( 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 143 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8131 (mp0) cc_final: 0.7757 (mp0) REVERT: A 129 ASP cc_start: 0.8209 (p0) cc_final: 0.7809 (p0) REVERT: A 132 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7896 (mtm-85) REVERT: A 245 CYS cc_start: 0.7606 (m) cc_final: 0.7319 (m) REVERT: A 293 GLU cc_start: 0.7187 (tt0) cc_final: 0.6927 (tt0) REVERT: B 73 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8410 (mt) REVERT: C 87 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7769 (mpp) REVERT: C 202 PHE cc_start: 0.8564 (m-80) cc_final: 0.8286 (m-80) REVERT: C 208 TYR cc_start: 0.5581 (t80) cc_final: 0.5360 (t80) REVERT: C 275 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8215 (mt) REVERT: C 324 GLU cc_start: 0.8510 (mp0) cc_final: 0.7933 (mp0) outliers start: 38 outliers final: 29 residues processed: 134 average time/residue: 0.1179 time to fit residues: 19.6363 Evaluate side-chains 129 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 125 VAL 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 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 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 310 ILE 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: 0.8980 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106840 restraints weight = 10143.075| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.82 r_work: 0.3200 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5704 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= 0.164 Angle : 0.719 10.121 9114 Z= 0.380 Chirality : 0.048 0.214 957 Planarity : 0.006 0.077 1188 Dihedral : 7.842 54.862 914 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.30 % Favored : 91.34 % Rotamer: Outliers : 4.51 % Allowed : 19.51 % Favored : 75.98 % 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: -2.34 (0.28), residues: 831 helix: -2.51 (0.44), residues: 96 sheet: -0.57 (0.55), residues: 87 loop : -1.67 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 132 TYR 0.027 0.002 TYR B 208 PHE 0.011 0.001 PHE B 330 TRP 0.006 0.001 TRP A 307 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 6669) covalent geometry : angle 0.71110 ( 9084) SS BOND : bond 0.00428 ( 15) SS BOND : angle 1.94289 ( 30) hydrogen bonds : bond 0.03512 ( 174) hydrogen bonds : angle 5.67373 ( 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 130 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8210 (mp0) cc_final: 0.7880 (mp0) REVERT: A 129 ASP cc_start: 0.8119 (p0) cc_final: 0.7536 (p0) REVERT: A 132 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7813 (mtm-85) REVERT: A 293 GLU cc_start: 0.7247 (tt0) cc_final: 0.6948 (tt0) REVERT: B 73 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8326 (mt) REVERT: B 310 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8444 (mt) REVERT: C 87 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7935 (mpp) REVERT: C 208 TYR cc_start: 0.5495 (t80) cc_final: 0.4772 (t80) REVERT: C 275 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8148 (mt) outliers start: 31 outliers final: 27 residues processed: 122 average time/residue: 0.1196 time to fit residues: 17.8367 Evaluate side-chains 126 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 274 VAL 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 119 LEU Chi-restraints excluded: chain B residue 125 VAL 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 298 GLN 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 206 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 310 ILE 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: 9.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 0.0040 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 2.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106673 restraints weight = 9985.091| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.80 r_work: 0.3202 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5801 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= 0.174 Angle : 0.722 9.753 9114 Z= 0.384 Chirality : 0.048 0.211 957 Planarity : 0.006 0.078 1188 Dihedral : 7.807 55.829 914 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.78 % Favored : 90.97 % Rotamer: Outliers : 5.09 % Allowed : 19.21 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % 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: -2.34 (0.28), residues: 831 helix: -2.27 (0.47), residues: 90 sheet: -0.57 (0.55), residues: 87 loop : -1.72 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 132 TYR 0.020 0.002 TYR B 208 PHE 0.013 0.001 PHE B 330 TRP 0.009 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6669) covalent geometry : angle 0.71519 ( 9084) SS BOND : bond 0.00379 ( 15) SS BOND : angle 1.92146 ( 30) hydrogen bonds : bond 0.03586 ( 174) hydrogen bonds : angle 5.67035 ( 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 131 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.8226 (mp0) cc_final: 0.7932 (mp0) REVERT: A 129 ASP cc_start: 0.8088 (p0) cc_final: 0.7510 (p0) REVERT: A 257 ARG cc_start: 0.8387 (ttt180) cc_final: 0.8149 (ttt-90) REVERT: A 293 GLU cc_start: 0.7236 (tt0) cc_final: 0.6897 (tt0) REVERT: B 73 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8337 (mt) REVERT: B 310 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8452 (mt) REVERT: C 87 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7969 (mpp) REVERT: C 202 PHE cc_start: 0.8561 (m-80) cc_final: 0.8270 (m-80) REVERT: C 207 PHE cc_start: 0.4412 (OUTLIER) cc_final: 0.3625 (p90) REVERT: C 275 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8229 (mt) outliers start: 35 outliers final: 26 residues processed: 122 average time/residue: 0.1184 time to fit residues: 17.8688 Evaluate side-chains 123 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 274 VAL 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 119 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 240 GLN 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 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 207 PHE 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: 6.9990 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 chunk 13 optimal weight: 0.0000 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111184 restraints weight = 9760.625| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.84 r_work: 0.3272 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6684 Z= 0.133 Angle : 0.690 8.494 9114 Z= 0.365 Chirality : 0.046 0.226 957 Planarity : 0.006 0.075 1188 Dihedral : 7.482 53.876 914 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.10 % Favored : 92.78 % Rotamer: Outliers : 4.08 % Allowed : 20.67 % Favored : 75.25 % 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: -2.26 (0.28), residues: 831 helix: -2.32 (0.47), residues: 96 sheet: -0.43 (0.55), residues: 87 loop : -1.66 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 132 TYR 0.017 0.001 TYR B 208 PHE 0.007 0.001 PHE B 330 TRP 0.005 0.000 TRP B 134 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6669) covalent geometry : angle 0.68528 ( 9084) SS BOND : bond 0.00301 ( 15) SS BOND : angle 1.53480 ( 30) hydrogen bonds : bond 0.03143 ( 174) hydrogen bonds : angle 5.21052 ( 486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1704.70 seconds wall clock time: 29 minutes 54.83 seconds (1794.83 seconds total)