Starting phenix.real_space_refine on Tue Mar 11 17:54:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e1e_30939/03_2025/7e1e_30939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e1e_30939/03_2025/7e1e_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_2025/7e1e_30939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e1e_30939/03_2025/7e1e_30939.map" model { file = "/net/cci-nas-00/data/ceres_data/7e1e_30939/03_2025/7e1e_30939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e1e_30939/03_2025/7e1e_30939.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.45, per 1000 atoms: 0.69 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: 1.70 Conformation dependent library (CDL) restraints added in 960.6 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: 0.89 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: 1.76 Time building geometry restraints manager: 2.01 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.490 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- 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 6669 Z= 0.479 Angle : 0.858 8.062 9084 Z= 0.502 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 : 11.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP C 178 HIS 0.003 0.001 HIS B 101 PHE 0.015 0.002 PHE C 127 TYR 0.012 0.002 TYR C 201 ARG 0.015 0.001 ARG B 257 *********************** 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 : 0.775 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: 0.2153 time to fit residues: 61.8446 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 : 0.726 ------------------------------------------------------------------------------- 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 68 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 0.0070 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.138942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.121976 restraints weight = 9535.466| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.83 r_work: 0.3421 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6669 Z= 0.214 Angle : 0.691 7.706 9084 Z= 0.368 Chirality : 0.047 0.230 957 Planarity : 0.006 0.073 1188 Dihedral : 9.776 92.592 937 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.26 % Favored : 93.50 % Rotamer: Outliers : 4.37 % Allowed : 13.83 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.26), residues: 831 helix: -3.14 (0.38), residues: 117 sheet: -0.70 (0.50), residues: 90 loop : -2.10 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.009 0.002 HIS B 255 PHE 0.012 0.001 PHE B 259 TYR 0.025 0.002 TYR A 208 ARG 0.005 0.001 ARG A 273 *********************** 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 155 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8461 (ptmm) cc_final: 0.8010 (ttmt) REVERT: A 293 GLU cc_start: 0.6739 (tt0) cc_final: 0.6247 (tt0) REVERT: B 79 GLN cc_start: 0.8928 (tt0) cc_final: 0.8587 (tt0) REVERT: B 142 ARG cc_start: 0.6970 (mtt90) cc_final: 0.6634 (mpt180) REVERT: B 158 ASP cc_start: 0.7488 (t0) cc_final: 0.6800 (t0) REVERT: B 212 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8449 (t80) REVERT: B 234 THR cc_start: 0.7145 (m) cc_final: 0.6824 (p) REVERT: B 293 GLU cc_start: 0.8021 (tt0) cc_final: 0.7778 (tt0) REVERT: B 307 TRP cc_start: 0.7160 (t-100) cc_final: 0.6661 (t-100) REVERT: B 310 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8400 (mt) REVERT: C 202 PHE cc_start: 0.8186 (m-80) cc_final: 0.7976 (m-80) REVERT: C 231 PHE cc_start: 0.8054 (t80) cc_final: 0.7768 (t80) outliers start: 30 outliers final: 14 residues processed: 145 average time/residue: 0.2146 time to fit residues: 39.9787 Evaluate side-chains 112 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 72 CYS 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 293 GLU 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 80 optimal weight: 9.9990 chunk 22 optimal weight: 0.0060 chunk 76 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 overall best weight: 2.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 122 ASN C 255 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111623 restraints weight = 9753.091| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.86 r_work: 0.3277 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6669 Z= 0.271 Angle : 0.673 7.158 9084 Z= 0.361 Chirality : 0.049 0.200 957 Planarity : 0.006 0.078 1188 Dihedral : 8.593 56.517 921 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 5.39 % Allowed : 15.57 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 12.82 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.27), residues: 831 helix: -2.93 (0.40), residues: 117 sheet: -0.41 (0.45), residues: 120 loop : -2.02 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 94 HIS 0.006 0.001 HIS B 255 PHE 0.013 0.002 PHE A 330 TYR 0.018 0.002 TYR A 208 ARG 0.005 0.001 ARG B 132 *********************** 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: 37 poor density : 108 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8459 (ptmm) REVERT: A 245 CYS cc_start: 0.6645 (m) cc_final: 0.6398 (m) REVERT: A 272 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8470 (pp) REVERT: A 293 GLU cc_start: 0.6893 (tt0) cc_final: 0.6340 (tt0) REVERT: B 142 ARG cc_start: 0.7324 (mtt90) cc_final: 0.7111 (mmt-90) REVERT: C 202 PHE cc_start: 0.8467 (m-80) cc_final: 0.8207 (m-80) REVERT: C 231 PHE cc_start: 0.8452 (t80) cc_final: 0.8162 (t80) REVERT: C 261 ASN cc_start: 0.8122 (m-40) cc_final: 0.7893 (m-40) outliers start: 37 outliers final: 19 residues processed: 133 average time/residue: 0.2363 time to fit residues: 39.5361 Evaluate side-chains 115 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 99 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 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 125 VAL Chi-restraints excluded: chain C residue 149 ASP 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 49 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.107054 restraints weight = 9974.828| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.87 r_work: 0.3205 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6669 Z= 0.296 Angle : 0.686 6.984 9084 Z= 0.364 Chirality : 0.049 0.202 957 Planarity : 0.006 0.081 1188 Dihedral : 8.322 53.892 920 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.94 % Favored : 91.94 % Rotamer: Outliers : 5.53 % Allowed : 15.14 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.28), residues: 831 helix: -2.13 (0.45), residues: 117 sheet: -0.31 (0.45), residues: 120 loop : -1.88 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 307 HIS 0.005 0.001 HIS B 255 PHE 0.015 0.002 PHE A 330 TYR 0.017 0.002 TYR A 208 ARG 0.006 0.001 ARG C 257 *********************** 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 153 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.657 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: 0.8719 (OUTLIER) cc_final: 0.8474 (ptmm) REVERT: A 191 GLU cc_start: 0.8412 (mp0) cc_final: 0.8197 (mp0) REVERT: A 245 CYS cc_start: 0.7233 (m) cc_final: 0.6993 (m) REVERT: A 272 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8668 (pp) REVERT: A 293 GLU cc_start: 0.7221 (tt0) cc_final: 0.6757 (tt0) REVERT: B 208 TYR cc_start: 0.5512 (t80) cc_final: 0.5220 (t80) REVERT: B 212 TYR cc_start: 0.9090 (OUTLIER) cc_final: 0.8832 (t80) REVERT: C 202 PHE cc_start: 0.8464 (m-80) cc_final: 0.8254 (m-80) REVERT: C 208 TYR cc_start: 0.5930 (t80) cc_final: 0.5012 (t80) REVERT: C 261 ASN cc_start: 0.8314 (m-40) cc_final: 0.8040 (m-40) REVERT: C 275 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7632 (mt) outliers start: 38 outliers final: 23 residues processed: 140 average time/residue: 0.2744 time to fit residues: 47.2074 Evaluate side-chains 124 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 147 THR 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 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 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 257 ARG 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 119 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 293 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.123201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105574 restraints weight = 9942.892| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.84 r_work: 0.3186 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6669 Z= 0.333 Angle : 0.714 9.489 9084 Z= 0.377 Chirality : 0.050 0.192 957 Planarity : 0.006 0.081 1188 Dihedral : 8.178 53.069 916 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.30 % Favored : 91.58 % Rotamer: Outliers : 5.53 % Allowed : 16.30 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.28), residues: 831 helix: -2.28 (0.43), residues: 114 sheet: -0.37 (0.45), residues: 120 loop : -1.84 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.016 0.002 PHE B 330 TYR 0.016 0.002 TYR B 208 ARG 0.021 0.001 ARG C 257 *********************** 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 139 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8408 (mp0) cc_final: 0.8181 (mp0) REVERT: A 272 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8667 (pp) REVERT: A 293 GLU cc_start: 0.7325 (tt0) cc_final: 0.7050 (tt0) REVERT: B 73 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8377 (mt) REVERT: B 212 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8762 (t80) REVERT: C 202 PHE cc_start: 0.8466 (m-80) cc_final: 0.8232 (m-80) REVERT: C 205 LYS cc_start: 0.7237 (mmtp) cc_final: 0.6985 (mmtp) REVERT: C 208 TYR cc_start: 0.5803 (t80) cc_final: 0.5408 (t80) outliers start: 38 outliers final: 25 residues processed: 126 average time/residue: 0.2883 time to fit residues: 44.0633 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 : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 180 ILE 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 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 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 298 GLN Chi-restraints excluded: chain C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain C residue 114 ARG 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 258 VAL Chi-restraints excluded: chain C residue 293 GLU Chi-restraints excluded: chain C residue 312 THR 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 8 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 79 optimal weight: 0.0020 chunk 31 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109089 restraints weight = 9742.036| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.85 r_work: 0.3241 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6669 Z= 0.224 Angle : 0.676 12.761 9084 Z= 0.355 Chirality : 0.047 0.203 957 Planarity : 0.006 0.078 1188 Dihedral : 7.748 51.663 914 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.86 % Favored : 92.78 % 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 : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 831 helix: -2.13 (0.44), residues: 114 sheet: -0.40 (0.54), residues: 87 loop : -1.62 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 307 HIS 0.004 0.001 HIS B 255 PHE 0.014 0.001 PHE B 184 TYR 0.015 0.001 TYR B 208 ARG 0.006 0.001 ARG B 132 *********************** 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 141 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8632 (pp) REVERT: A 293 GLU cc_start: 0.7174 (tt0) cc_final: 0.6730 (tt0) REVERT: B 73 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 212 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.8777 (t80) REVERT: B 310 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8406 (mt) REVERT: C 205 LYS cc_start: 0.7063 (mmtp) cc_final: 0.6767 (mmtp) REVERT: C 208 TYR cc_start: 0.5349 (t80) cc_final: 0.5061 (t80) REVERT: C 275 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7406 (mt) REVERT: C 324 GLU cc_start: 0.8342 (mp0) cc_final: 0.8046 (mp0) outliers start: 33 outliers final: 18 residues processed: 127 average time/residue: 0.2529 time to fit residues: 39.9030 Evaluate side-chains 115 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE 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 148 ASP 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 C residue 64 LYS Chi-restraints excluded: chain C residue 66 LYS 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 258 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 312 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.124852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107115 restraints weight = 9866.418| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.86 r_work: 0.3213 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6669 Z= 0.273 Angle : 0.695 10.155 9084 Z= 0.367 Chirality : 0.048 0.199 957 Planarity : 0.006 0.080 1188 Dihedral : 7.795 51.878 914 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.18 % Favored : 91.58 % Rotamer: Outliers : 5.09 % Allowed : 18.05 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.28), residues: 831 helix: -2.27 (0.42), residues: 114 sheet: -0.47 (0.54), residues: 87 loop : -1.51 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.013 0.001 PHE B 330 TYR 0.015 0.002 TYR B 208 ARG 0.005 0.001 ARG B 132 *********************** 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 139 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.7963 (p0) cc_final: 0.7609 (p0) REVERT: A 132 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7931 (mtm-85) REVERT: A 272 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8675 (pp) REVERT: A 293 GLU cc_start: 0.7255 (tt0) cc_final: 0.6859 (tt0) REVERT: B 73 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8302 (mt) REVERT: B 212 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.8761 (t80) REVERT: B 257 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6195 (tmm-80) REVERT: C 87 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8068 (mpp) REVERT: C 205 LYS cc_start: 0.7133 (mmtp) cc_final: 0.6859 (mmtp) REVERT: C 275 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7634 (mt) outliers start: 35 outliers final: 25 residues processed: 126 average time/residue: 0.2588 time to fit residues: 40.2586 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 : 0.666 ------------------------------------------------------------------------------- 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 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 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 298 GLN 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 149 ASP 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 312 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 22 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.123742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106355 restraints weight = 9892.970| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.81 r_work: 0.3196 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 6669 Z= 0.314 Angle : 0.709 7.588 9084 Z= 0.375 Chirality : 0.049 0.195 957 Planarity : 0.007 0.080 1188 Dihedral : 7.813 53.334 914 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.54 % Favored : 91.34 % Rotamer: Outliers : 5.24 % Allowed : 19.07 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.28), residues: 831 helix: -2.30 (0.42), residues: 114 sheet: -0.50 (0.53), residues: 87 loop : -1.60 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.014 0.002 PHE B 330 TYR 0.028 0.002 TYR C 208 ARG 0.006 0.001 ARG A 257 *********************** 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 133 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7349 (tt0) cc_final: 0.7005 (tt0) REVERT: B 73 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8356 (mt) REVERT: B 212 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8706 (t80) REVERT: B 310 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8463 (mt) REVERT: C 87 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8101 (mpp) REVERT: C 202 PHE cc_start: 0.8487 (m-80) cc_final: 0.8211 (m-80) REVERT: C 275 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7651 (mt) REVERT: C 324 GLU cc_start: 0.8377 (mp0) cc_final: 0.7830 (mp0) outliers start: 36 outliers final: 28 residues processed: 121 average time/residue: 0.2569 time to fit residues: 38.4946 Evaluate side-chains 126 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 93 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 212 TYR 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 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 149 ASP 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 312 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.127277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110073 restraints weight = 9883.970| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.82 r_work: 0.3252 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6669 Z= 0.215 Angle : 0.670 7.182 9084 Z= 0.356 Chirality : 0.047 0.203 957 Planarity : 0.007 0.076 1188 Dihedral : 7.517 52.089 914 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.78 % Favored : 91.10 % Rotamer: Outliers : 4.22 % Allowed : 19.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.28), residues: 831 helix: -1.99 (0.48), residues: 96 sheet: -0.45 (0.54), residues: 87 loop : -1.56 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.004 0.001 HIS B 255 PHE 0.009 0.001 PHE A 330 TYR 0.019 0.001 TYR B 208 ARG 0.006 0.001 ARG B 132 *********************** 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 132 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ASP cc_start: 0.8109 (p0) cc_final: 0.7676 (p0) REVERT: A 245 CYS cc_start: 0.7550 (m) cc_final: 0.7311 (m) REVERT: A 257 ARG cc_start: 0.8048 (tmt170) cc_final: 0.7734 (tmt-80) REVERT: A 293 GLU cc_start: 0.7238 (tt0) cc_final: 0.6835 (tt0) REVERT: B 73 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8282 (mt) REVERT: B 212 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8707 (t80) REVERT: B 310 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8465 (mt) REVERT: C 87 MET cc_start: 0.8397 (mpp) cc_final: 0.8081 (mpp) REVERT: C 275 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7499 (mt) REVERT: C 324 GLU cc_start: 0.8294 (mp0) cc_final: 0.7996 (mp0) outliers start: 29 outliers final: 24 residues processed: 122 average time/residue: 0.2613 time to fit residues: 39.5785 Evaluate side-chains 122 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE 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 212 TYR 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 66 LYS 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 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 180 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 312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 2 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106527 restraints weight = 10039.636| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.82 r_work: 0.3196 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6669 Z= 0.328 Angle : 0.730 9.452 9084 Z= 0.388 Chirality : 0.050 0.210 957 Planarity : 0.007 0.078 1188 Dihedral : 7.750 53.432 914 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.90 % Favored : 90.97 % Rotamer: Outliers : 4.51 % Allowed : 20.38 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.28), residues: 831 helix: -2.14 (0.46), residues: 96 sheet: -0.51 (0.54), residues: 87 loop : -1.62 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 307 HIS 0.005 0.001 HIS B 187 PHE 0.014 0.002 PHE B 330 TYR 0.030 0.002 TYR C 208 ARG 0.006 0.001 ARG B 132 ********************** 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 130 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.685 Fit side-chains revert: symmetry clash 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: 0.7931 (p0) REVERT: A 293 GLU cc_start: 0.7309 (tt0) cc_final: 0.6992 (tt0) REVERT: B 73 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8378 (mt) REVERT: B 212 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8681 (t80) REVERT: B 257 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6168 (tmm-80) REVERT: B 310 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8417 (mt) REVERT: C 87 MET cc_start: 0.8441 (mpp) cc_final: 0.8090 (mpp) REVERT: C 202 PHE cc_start: 0.8549 (m-80) cc_final: 0.8265 (m-80) REVERT: C 257 ARG cc_start: 0.6946 (tmt170) cc_final: 0.6561 (ttm-80) REVERT: C 275 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7676 (mt) outliers start: 31 outliers final: 25 residues processed: 122 average time/residue: 0.2862 time to fit residues: 42.5173 Evaluate side-chains 127 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE 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 125 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 257 ARG 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 66 LYS 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 149 ASP Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 180 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 312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106497 restraints weight = 10166.110| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.84 r_work: 0.3196 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6669 Z= 0.295 Angle : 0.720 9.642 9084 Z= 0.383 Chirality : 0.049 0.215 957 Planarity : 0.007 0.079 1188 Dihedral : 7.704 54.093 914 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.03 % Favored : 90.85 % Rotamer: Outliers : 4.95 % Allowed : 20.09 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 10.26 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.28), residues: 831 helix: -2.17 (0.46), residues: 96 sheet: -0.50 (0.55), residues: 87 loop : -1.64 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 307 HIS 0.004 0.001 HIS B 187 PHE 0.014 0.001 PHE B 330 TYR 0.026 0.002 TYR C 208 ARG 0.006 0.001 ARG B 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3563.04 seconds wall clock time: 61 minutes 42.40 seconds (3702.40 seconds total)