Starting phenix.real_space_refine on Wed Apr 30 18:47:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4t_17428/04_2025/8p4t_17428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4t_17428/04_2025/8p4t_17428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p4t_17428/04_2025/8p4t_17428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4t_17428/04_2025/8p4t_17428.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4t_17428/04_2025/8p4t_17428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4t_17428/04_2025/8p4t_17428.cif" } resolution = 2.96 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 Na 1 4.78 5 C 6333 2.51 5 N 1593 2.21 5 O 1983 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9976 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1330 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "a" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1461 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 3, 'TRANS': 174} Chain breaks: 1 Chain: "SA" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 265 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' NA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, G, I, H, J, K, L, SB, SC, b, c Time building chain proxies: 5.53, per 1000 atoms: 0.55 Number of scatterers: 9976 At special positions: 0 Unit cell: (95.584, 96.408, 129.368, 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) S 66 16.00 Na 1 11.00 O 1983 8.00 N 1593 7.00 C 6333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS a 241 " - pdb=" SG CYS a 254 " distance=2.03 Simple disulfide: pdb=" SG CYS a 263 " - pdb=" SG CYS a 272 " distance=2.04 Simple disulfide: pdb=" SG CYS a 326 " - pdb=" SG CYS a 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 89 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS b 241 " - pdb=" SG CYS b 254 " distance=2.03 Simple disulfide: pdb=" SG CYS c 241 " - pdb=" SG CYS c 254 " distance=2.03 Simple disulfide: pdb=" SG CYS b 263 " - pdb=" SG CYS b 272 " distance=2.04 Simple disulfide: pdb=" SG CYS c 263 " - pdb=" SG CYS c 272 " distance=2.04 Simple disulfide: pdb=" SG CYS b 326 " - pdb=" SG CYS b 347 " distance=2.03 Simple disulfide: pdb=" SG CYS c 326 " - pdb=" SG CYS c 347 " 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 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN H 4 " - " MAN H 5 " " MAN J 4 " - " MAN J 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA E 3 " - " MAN E 6 " " MAN E 6 " - " MAN E 7 " " BMA H 3 " - " MAN H 6 " " MAN H 6 " - " MAN H 7 " " BMA J 3 " - " MAN J 6 " " MAN J 6 " - " MAN J 7 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " BETA1-6 " NAG D 1 " - " FUC D 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 5 " " NAG I 1 " - " FUC I 5 " NAG-ASN " NAG A 301 " - " ASN A 73 " " NAG A 302 " - " ASN A 104 " " NAG A 303 " - " ASN A 194 " " NAG A 304 " - " ASN A 93 " " NAG B 301 " - " ASN B 73 " " NAG B 302 " - " ASN B 104 " " NAG B 303 " - " ASN B 194 " " NAG B 304 " - " ASN B 93 " " NAG C 301 " - " ASN C 73 " " NAG C 302 " - " ASN C 104 " " NAG C 303 " - " ASN C 194 " " NAG C 304 " - " ASN C 93 " " NAG D 1 " - " ASN A 112 " " NAG E 1 " - " ASN A 148 " " NAG F 1 " - " ASN a 335 " " NAG G 1 " - " ASN B 112 " " NAG H 1 " - " ASN B 148 " " NAG I 1 " - " ASN C 112 " " NAG J 1 " - " ASN C 148 " " NAG K 1 " - " ASN b 335 " " NAG L 1 " - " ASN c 335 " " NAG a 501 " - " ASN a 352 " " NAG a 502 " - " ASN a 327 " " NAG a 503 " - " ASN a 357 " " NAG b 501 " - " ASN b 352 " " NAG b 502 " - " ASN b 327 " " NAG b 503 " - " ASN b 357 " " NAG c 501 " - " ASN c 352 " " NAG c 502 " - " ASN c 327 " " NAG c 503 " - " ASN c 357 " Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 55.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 60 through 64 removed outlier: 4.500A pdb=" N GLY A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 60 through 64' Processing helix chain 'A' and resid 74 through 77 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.512A pdb=" N PHE A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.853A pdb=" N THR A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'a' and resid 256 through 262 Processing helix chain 'a' and resid 269 through 288 Processing helix chain 'a' and resid 291 through 298 removed outlier: 3.783A pdb=" N SER a 295 " --> pdb=" O GLU a 291 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE a 296 " --> pdb=" O ALA a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 302 through 307 removed outlier: 3.957A pdb=" N ILE a 306 " --> pdb=" O ARG a 302 " (cutoff:3.500A) Processing helix chain 'a' and resid 308 through 322 removed outlier: 3.519A pdb=" N LEU a 312 " --> pdb=" O SER a 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 357 through 360 Processing helix chain 'a' and resid 361 through 388 Processing helix chain 'a' and resid 389 through 409 removed outlier: 3.784A pdb=" N LEU a 409 " --> pdb=" O PHE a 405 " (cutoff:3.500A) Processing helix chain 'SA' and resid 3 through 8 removed outlier: 3.632A pdb=" N ILESA 8 " --> pdb=" O VALSA 4 " (cutoff:3.500A) Processing helix chain 'SA' and resid 9 through 12 removed outlier: 3.801A pdb=" N LEUSA 12 " --> pdb=" O PROSA 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 9 through 12' Processing helix chain 'SA' and resid 14 through 35 Processing helix chain 'B' and resid 61 through 64 No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 120 through 135 removed outlier: 3.512A pdb=" N PHE B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.853A pdb=" N THR B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'C' and resid 61 through 64 No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 120 through 135 removed outlier: 3.513A pdb=" N PHE C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU C 129 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N PHE C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 174 removed outlier: 3.853A pdb=" N THR C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'SB' and resid 3 through 8 removed outlier: 3.633A pdb=" N ILESB 8 " --> pdb=" O VALSB 4 " (cutoff:3.500A) Processing helix chain 'SB' and resid 9 through 12 removed outlier: 3.801A pdb=" N LEUSB 12 " --> pdb=" O PROSB 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'SB' and resid 9 through 12' Processing helix chain 'SB' and resid 14 through 35 Processing helix chain 'SC' and resid 3 through 8 removed outlier: 3.631A pdb=" N ILESC 8 " --> pdb=" O VALSC 4 " (cutoff:3.500A) Processing helix chain 'SC' and resid 9 through 12 removed outlier: 3.801A pdb=" N LEUSC 12 " --> pdb=" O PROSC 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 9 through 12' Processing helix chain 'SC' and resid 14 through 35 Processing helix chain 'b' and resid 256 through 262 Processing helix chain 'b' and resid 269 through 288 Processing helix chain 'b' and resid 291 through 298 removed outlier: 3.783A pdb=" N SER b 295 " --> pdb=" O GLU b 291 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE b 296 " --> pdb=" O ALA b 292 " (cutoff:3.500A) Processing helix chain 'b' and resid 302 through 307 removed outlier: 3.957A pdb=" N ILE b 306 " --> pdb=" O ARG b 302 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 322 removed outlier: 3.518A pdb=" N LEU b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 357 through 360 Processing helix chain 'b' and resid 361 through 388 Processing helix chain 'b' and resid 389 through 409 removed outlier: 3.783A pdb=" N LEU b 409 " --> pdb=" O PHE b 405 " (cutoff:3.500A) Processing helix chain 'c' and resid 256 through 262 Processing helix chain 'c' and resid 269 through 288 Processing helix chain 'c' and resid 291 through 298 removed outlier: 3.783A pdb=" N SER c 295 " --> pdb=" O GLU c 291 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE c 296 " --> pdb=" O ALA c 292 " (cutoff:3.500A) Processing helix chain 'c' and resid 302 through 307 removed outlier: 3.958A pdb=" N ILE c 306 " --> pdb=" O ARG c 302 " (cutoff:3.500A) Processing helix chain 'c' and resid 308 through 322 removed outlier: 3.519A pdb=" N LEU c 312 " --> pdb=" O SER c 308 " (cutoff:3.500A) Processing helix chain 'c' and resid 357 through 360 Processing helix chain 'c' and resid 361 through 388 Processing helix chain 'c' and resid 389 through 409 removed outlier: 3.784A pdb=" N LEU c 409 " --> pdb=" O PHE c 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 246 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 84 removed outlier: 4.097A pdb=" N ARG A 183 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 246 through 248 Processing sheet with id=AA4, first strand: chain 'a' and resid 350 through 351 Processing sheet with id=AA5, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.096A pdb=" N ARG B 183 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 246 through 248 Processing sheet with id=AA7, first strand: chain 'C' and resid 82 through 84 removed outlier: 4.097A pdb=" N ARG C 183 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 350 through 351 Processing sheet with id=AA9, first strand: chain 'c' and resid 350 through 351 486 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 4.01 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: 2969 1.34 - 1.46: 2498 1.46 - 1.58: 4595 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 10164 Sorted by residual: bond pdb=" CG1 ILE B 154 " pdb=" CD1 ILE B 154 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.25e+00 bond pdb=" CG1 ILE A 154 " pdb=" CD1 ILE A 154 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.24e+00 bond pdb=" CG1 ILE C 154 " pdb=" CD1 ILE C 154 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.23e+00 bond pdb=" CG ARG a 276 " pdb=" CD ARG a 276 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.95e-01 bond pdb=" CG ARG b 276 " pdb=" CD ARG b 276 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.68e-01 ... (remaining 10159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 13162 1.22 - 2.45: 462 2.45 - 3.67: 74 3.67 - 4.89: 18 4.89 - 6.12: 6 Bond angle restraints: 13722 Sorted by residual: angle pdb=" C LEU A 126 " pdb=" N PHE A 127 " pdb=" CA PHE A 127 " ideal model delta sigma weight residual 122.38 116.26 6.12 1.81e+00 3.05e-01 1.14e+01 angle pdb=" C LEU B 126 " pdb=" N PHE B 127 " pdb=" CA PHE B 127 " ideal model delta sigma weight residual 122.38 116.27 6.11 1.81e+00 3.05e-01 1.14e+01 angle pdb=" N PHE A 127 " pdb=" CA PHE A 127 " pdb=" CB PHE A 127 " ideal model delta sigma weight residual 110.44 115.59 -5.15 1.53e+00 4.27e-01 1.13e+01 angle pdb=" C LEU C 126 " pdb=" N PHE C 127 " pdb=" CA PHE C 127 " ideal model delta sigma weight residual 122.38 116.29 6.09 1.81e+00 3.05e-01 1.13e+01 angle pdb=" N PHE B 127 " pdb=" CA PHE B 127 " pdb=" CB PHE B 127 " ideal model delta sigma weight residual 110.44 115.57 -5.13 1.53e+00 4.27e-01 1.12e+01 ... (remaining 13717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.20: 6006 13.20 - 26.41: 694 26.41 - 39.61: 227 39.61 - 52.82: 24 52.82 - 66.02: 15 Dihedral angle restraints: 6966 sinusoidal: 3633 harmonic: 3333 Sorted by residual: dihedral pdb=" CB CYS a 263 " pdb=" SG CYS a 263 " pdb=" SG CYS a 272 " pdb=" CB CYS a 272 " ideal model delta sinusoidal sigma weight residual -86.00 -52.79 -33.21 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CB CYS c 263 " pdb=" SG CYS c 263 " pdb=" SG CYS c 272 " pdb=" CB CYS c 272 " ideal model delta sinusoidal sigma weight residual -86.00 -52.81 -33.19 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CB CYS b 263 " pdb=" SG CYS b 263 " pdb=" SG CYS b 272 " pdb=" CB CYS b 272 " ideal model delta sinusoidal sigma weight residual -86.00 -52.83 -33.17 1 1.00e+01 1.00e-02 1.56e+01 ... (remaining 6963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1340 0.039 - 0.077: 297 0.077 - 0.116: 85 0.116 - 0.154: 33 0.154 - 0.193: 3 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CA ASN a 327 " pdb=" N ASN a 327 " pdb=" C ASN a 327 " pdb=" CB ASN a 327 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA ASN c 327 " pdb=" N ASN c 327 " pdb=" C ASN c 327 " pdb=" CB ASN c 327 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA ASN b 327 " pdb=" N ASN b 327 " pdb=" C ASN b 327 " pdb=" CB ASN b 327 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 1755 not shown) Planarity restraints: 1647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP c 348 " 0.014 2.00e-02 2.50e+03 1.31e-02 4.28e+00 pdb=" CG TRP c 348 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP c 348 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP c 348 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP c 348 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP c 348 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP c 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 348 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP c 348 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 348 " 0.014 2.00e-02 2.50e+03 1.31e-02 4.28e+00 pdb=" CG TRP a 348 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP a 348 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP a 348 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP a 348 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP a 348 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 348 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 348 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 348 " -0.014 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" CG TRP b 348 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP b 348 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP b 348 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP b 348 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP b 348 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP b 348 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 348 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 348 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP b 348 " -0.001 2.00e-02 2.50e+03 ... (remaining 1644 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1006 2.75 - 3.29: 9769 3.29 - 3.83: 16525 3.83 - 4.36: 20122 4.36 - 4.90: 33203 Nonbonded interactions: 80625 Sorted by model distance: nonbonded pdb=" OH TYR c 333 " pdb=" O7 NAG L 1 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR a 333 " pdb=" O7 NAG F 1 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR b 333 " pdb=" O7 NAG K 1 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 79 " pdb=" OD1 ASN b 281 " model vdw 2.235 3.040 nonbonded pdb=" OE2 GLU A 212 " pdb="NA NA A 305 " model vdw 2.290 2.470 ... (remaining 80620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 221 or resid 301 through 304)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'SA' selection = chain 'SB' selection = chain 'SC' } 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: 1.140 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.400 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 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 : 0.002 0.044 10242 Z= 0.121 Angle : 0.587 7.624 13941 Z= 0.307 Chirality : 0.040 0.193 1758 Planarity : 0.003 0.024 1617 Dihedral : 11.922 66.024 4731 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1098 helix: 0.61 (0.22), residues: 498 sheet: -0.24 (0.47), residues: 105 loop : 0.08 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP c 348 HIS 0.005 0.001 HIS a 240 PHE 0.017 0.001 PHE a 402 TYR 0.015 0.001 TYR A 156 ARG 0.002 0.000 ARG c 276 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 30) link_NAG-ASN : angle 2.36212 ( 90) link_ALPHA1-6 : bond 0.00647 ( 6) link_ALPHA1-6 : angle 1.60312 ( 18) link_BETA1-4 : bond 0.00351 ( 15) link_BETA1-4 : angle 1.51765 ( 45) link_ALPHA1-2 : bond 0.00616 ( 3) link_ALPHA1-2 : angle 1.22461 ( 9) link_ALPHA1-3 : bond 0.00848 ( 6) link_ALPHA1-3 : angle 1.48549 ( 18) hydrogen bonds : bond 0.14572 ( 486) hydrogen bonds : angle 6.59247 ( 1377) link_BETA1-6 : bond 0.00308 ( 3) link_BETA1-6 : angle 1.20527 ( 9) SS BOND : bond 0.00441 ( 15) SS BOND : angle 1.31306 ( 30) covalent geometry : bond 0.00240 (10164) covalent geometry : angle 0.54166 (13722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.105 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 329 average time/residue: 1.2870 time to fit residues: 451.3470 Evaluate side-chains 198 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain c residue 366 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 281 ASN SA 17 ASN B 86 GLN SC 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.083642 restraints weight = 17061.214| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.68 r_work: 0.2858 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10242 Z= 0.180 Angle : 0.640 6.343 13941 Z= 0.328 Chirality : 0.042 0.161 1758 Planarity : 0.004 0.044 1617 Dihedral : 6.674 157.902 2474 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.52 % Allowed : 12.10 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1098 helix: 1.46 (0.23), residues: 492 sheet: 0.50 (0.56), residues: 81 loop : 0.32 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 348 HIS 0.007 0.001 HIS B 199 PHE 0.029 0.002 PHE a 402 TYR 0.017 0.002 TYR C 156 ARG 0.005 0.001 ARG c 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 30) link_NAG-ASN : angle 2.17035 ( 90) link_ALPHA1-6 : bond 0.00570 ( 6) link_ALPHA1-6 : angle 1.62014 ( 18) link_BETA1-4 : bond 0.00355 ( 15) link_BETA1-4 : angle 1.61083 ( 45) link_ALPHA1-2 : bond 0.00587 ( 3) link_ALPHA1-2 : angle 1.33600 ( 9) link_ALPHA1-3 : bond 0.00737 ( 6) link_ALPHA1-3 : angle 1.65065 ( 18) hydrogen bonds : bond 0.05586 ( 486) hydrogen bonds : angle 5.28896 ( 1377) link_BETA1-6 : bond 0.00163 ( 3) link_BETA1-6 : angle 1.39769 ( 9) SS BOND : bond 0.00331 ( 15) SS BOND : angle 0.77155 ( 30) covalent geometry : bond 0.00401 (10164) covalent geometry : angle 0.60477 (13722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7827 (t0) cc_final: 0.7578 (t0) REVERT: A 182 ASP cc_start: 0.8990 (t0) cc_final: 0.8535 (t0) REVERT: A 218 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8526 (mtp85) REVERT: B 120 ASP cc_start: 0.7915 (t0) cc_final: 0.7666 (t0) REVERT: B 183 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6969 (mmp80) REVERT: B 196 THR cc_start: 0.8579 (m) cc_final: 0.8191 (p) REVERT: B 219 LYS cc_start: 0.8590 (tptp) cc_final: 0.8276 (tptp) REVERT: C 120 ASP cc_start: 0.7848 (t0) cc_final: 0.7599 (t0) REVERT: C 144 LYS cc_start: 0.7998 (mttt) cc_final: 0.7533 (mtpm) REVERT: C 155 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7777 (mt-10) REVERT: C 168 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: C 182 ASP cc_start: 0.9143 (t0) cc_final: 0.8746 (t0) outliers start: 37 outliers final: 16 residues processed: 237 average time/residue: 1.4880 time to fit residues: 375.8447 Evaluate side-chains 208 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain c residue 294 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 304 ASN ** SA 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN c 264 ASN c 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.123722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.084474 restraints weight = 17176.086| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.57 r_work: 0.2864 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10242 Z= 0.144 Angle : 0.608 7.373 13941 Z= 0.307 Chirality : 0.041 0.143 1758 Planarity : 0.004 0.033 1617 Dihedral : 5.657 53.197 2469 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.71 % Allowed : 14.57 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1098 helix: 1.50 (0.23), residues: 510 sheet: 0.61 (0.53), residues: 81 loop : 0.31 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 348 HIS 0.005 0.000 HIS B 199 PHE 0.022 0.001 PHE b 402 TYR 0.011 0.001 TYR C 156 ARG 0.008 0.001 ARG A 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 30) link_NAG-ASN : angle 2.07349 ( 90) link_ALPHA1-6 : bond 0.00593 ( 6) link_ALPHA1-6 : angle 1.62383 ( 18) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 1.50432 ( 45) link_ALPHA1-2 : bond 0.00664 ( 3) link_ALPHA1-2 : angle 1.24770 ( 9) link_ALPHA1-3 : bond 0.00803 ( 6) link_ALPHA1-3 : angle 1.58162 ( 18) hydrogen bonds : bond 0.04840 ( 486) hydrogen bonds : angle 4.95751 ( 1377) link_BETA1-6 : bond 0.00053 ( 3) link_BETA1-6 : angle 1.44484 ( 9) SS BOND : bond 0.00483 ( 15) SS BOND : angle 1.17267 ( 30) covalent geometry : bond 0.00306 (10164) covalent geometry : angle 0.57290 (13722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7851 (t0) cc_final: 0.7515 (t0) REVERT: A 218 ARG cc_start: 0.8874 (mtp85) cc_final: 0.8210 (mtp85) REVERT: A 219 LYS cc_start: 0.8596 (tptp) cc_final: 0.8293 (tptp) REVERT: B 74 MET cc_start: 0.8797 (mmt) cc_final: 0.8341 (mmt) REVERT: B 120 ASP cc_start: 0.7948 (t0) cc_final: 0.7603 (t0) REVERT: B 144 LYS cc_start: 0.8258 (mtpt) cc_final: 0.8049 (mtpp) REVERT: B 196 THR cc_start: 0.8753 (m) cc_final: 0.8413 (p) REVERT: C 120 ASP cc_start: 0.7937 (t0) cc_final: 0.7579 (t0) REVERT: C 155 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7807 (mt-10) REVERT: C 168 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: C 182 ASP cc_start: 0.9131 (t0) cc_final: 0.8708 (t0) outliers start: 39 outliers final: 20 residues processed: 214 average time/residue: 1.3383 time to fit residues: 308.2275 Evaluate side-chains 211 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain SC residue 35 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 294 SER Chi-restraints excluded: chain c residue 337 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN c 264 ASN c 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.084352 restraints weight = 16990.463| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.54 r_work: 0.2902 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10242 Z= 0.134 Angle : 0.592 8.425 13941 Z= 0.297 Chirality : 0.040 0.141 1758 Planarity : 0.004 0.028 1617 Dihedral : 5.597 53.420 2469 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.95 % Allowed : 16.19 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1098 helix: 1.51 (0.23), residues: 528 sheet: 0.87 (0.46), residues: 105 loop : 0.41 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 348 HIS 0.004 0.000 HIS B 199 PHE 0.019 0.001 PHE a 402 TYR 0.013 0.001 TYR C 156 ARG 0.006 0.000 ARG A 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 30) link_NAG-ASN : angle 2.04431 ( 90) link_ALPHA1-6 : bond 0.00587 ( 6) link_ALPHA1-6 : angle 1.61616 ( 18) link_BETA1-4 : bond 0.00364 ( 15) link_BETA1-4 : angle 1.50406 ( 45) link_ALPHA1-2 : bond 0.00626 ( 3) link_ALPHA1-2 : angle 1.25375 ( 9) link_ALPHA1-3 : bond 0.00776 ( 6) link_ALPHA1-3 : angle 1.54763 ( 18) hydrogen bonds : bond 0.04534 ( 486) hydrogen bonds : angle 4.76087 ( 1377) link_BETA1-6 : bond 0.00069 ( 3) link_BETA1-6 : angle 1.37206 ( 9) SS BOND : bond 0.00383 ( 15) SS BOND : angle 1.32945 ( 30) covalent geometry : bond 0.00292 (10164) covalent geometry : angle 0.55520 (13722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.7995 (t0) cc_final: 0.7682 (t0) REVERT: A 218 ARG cc_start: 0.8898 (mtp85) cc_final: 0.8317 (mtp85) REVERT: B 120 ASP cc_start: 0.7964 (t0) cc_final: 0.7590 (t0) REVERT: B 196 THR cc_start: 0.8859 (m) cc_final: 0.8574 (p) REVERT: B 217 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.9053 (m) REVERT: B 218 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8319 (mtm180) REVERT: B 219 LYS cc_start: 0.8571 (tptp) cc_final: 0.8295 (tptp) REVERT: C 120 ASP cc_start: 0.8021 (t0) cc_final: 0.7625 (t0) REVERT: C 155 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7767 (mt-10) REVERT: C 159 THR cc_start: 0.8220 (t) cc_final: 0.7991 (t) REVERT: C 168 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: C 182 ASP cc_start: 0.9077 (t0) cc_final: 0.8630 (t0) REVERT: C 218 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8196 (mtp85) REVERT: SB 25 MET cc_start: 0.8219 (mmm) cc_final: 0.7947 (mmm) outliers start: 31 outliers final: 21 residues processed: 214 average time/residue: 1.2352 time to fit residues: 283.1409 Evaluate side-chains 203 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain SA residue 35 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 260 ILE Chi-restraints excluded: chain c residue 294 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 304 ASN B 86 GLN C 71 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.077602 restraints weight = 17119.727| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.58 r_work: 0.2761 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10242 Z= 0.245 Angle : 0.674 9.608 13941 Z= 0.335 Chirality : 0.043 0.163 1758 Planarity : 0.004 0.047 1617 Dihedral : 5.879 56.164 2469 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.10 % Allowed : 16.29 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1098 helix: 1.47 (0.23), residues: 531 sheet: 0.21 (0.45), residues: 123 loop : 0.34 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 348 HIS 0.003 0.001 HIS A 214 PHE 0.013 0.001 PHE b 402 TYR 0.012 0.002 TYR C 156 ARG 0.006 0.001 ARG C 218 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 30) link_NAG-ASN : angle 2.26754 ( 90) link_ALPHA1-6 : bond 0.00525 ( 6) link_ALPHA1-6 : angle 1.58399 ( 18) link_BETA1-4 : bond 0.00388 ( 15) link_BETA1-4 : angle 1.62695 ( 45) link_ALPHA1-2 : bond 0.00501 ( 3) link_ALPHA1-2 : angle 1.34524 ( 9) link_ALPHA1-3 : bond 0.00649 ( 6) link_ALPHA1-3 : angle 1.71794 ( 18) hydrogen bonds : bond 0.05166 ( 486) hydrogen bonds : angle 4.95051 ( 1377) link_BETA1-6 : bond 0.00188 ( 3) link_BETA1-6 : angle 1.60401 ( 9) SS BOND : bond 0.00491 ( 15) SS BOND : angle 1.50016 ( 30) covalent geometry : bond 0.00570 (10164) covalent geometry : angle 0.63561 (13722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8334 (t0) cc_final: 0.8038 (t0) REVERT: A 168 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: B 120 ASP cc_start: 0.8266 (t0) cc_final: 0.7789 (t0) REVERT: B 121 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7696 (mtp-110) REVERT: B 182 ASP cc_start: 0.8829 (t0) cc_final: 0.8570 (t0) REVERT: B 196 THR cc_start: 0.9039 (m) cc_final: 0.8739 (p) REVERT: B 218 ARG cc_start: 0.8869 (mtm180) cc_final: 0.8655 (mtm180) REVERT: C 105 LYS cc_start: 0.9330 (tttp) cc_final: 0.9108 (tmtm) REVERT: C 120 ASP cc_start: 0.8314 (t0) cc_final: 0.7827 (t0) REVERT: C 155 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7796 (mt-10) REVERT: C 159 THR cc_start: 0.8540 (t) cc_final: 0.8228 (p) REVERT: SB 25 MET cc_start: 0.8426 (mmm) cc_final: 0.8155 (mmm) REVERT: c 364 ASP cc_start: 0.8937 (m-30) cc_final: 0.8500 (t0) REVERT: c 367 ASP cc_start: 0.8960 (t0) cc_final: 0.8745 (t0) outliers start: 43 outliers final: 23 residues processed: 212 average time/residue: 1.3173 time to fit residues: 298.7516 Evaluate side-chains 202 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 294 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 117 GLN B 86 GLN C 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080474 restraints weight = 17133.215| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.64 r_work: 0.2815 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10242 Z= 0.135 Angle : 0.619 10.507 13941 Z= 0.307 Chirality : 0.040 0.162 1758 Planarity : 0.004 0.081 1617 Dihedral : 5.691 53.938 2469 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.81 % Allowed : 17.52 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1098 helix: 1.66 (0.23), residues: 528 sheet: 0.25 (0.45), residues: 123 loop : 0.22 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 226 HIS 0.002 0.000 HIS A 199 PHE 0.013 0.001 PHE b 402 TYR 0.012 0.001 TYR C 156 ARG 0.008 0.001 ARG A 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 30) link_NAG-ASN : angle 2.01353 ( 90) link_ALPHA1-6 : bond 0.00626 ( 6) link_ALPHA1-6 : angle 1.59973 ( 18) link_BETA1-4 : bond 0.00358 ( 15) link_BETA1-4 : angle 1.44006 ( 45) link_ALPHA1-2 : bond 0.00638 ( 3) link_ALPHA1-2 : angle 1.26622 ( 9) link_ALPHA1-3 : bond 0.00916 ( 6) link_ALPHA1-3 : angle 1.57902 ( 18) hydrogen bonds : bond 0.04531 ( 486) hydrogen bonds : angle 4.75069 ( 1377) link_BETA1-6 : bond 0.00063 ( 3) link_BETA1-6 : angle 1.38868 ( 9) SS BOND : bond 0.00351 ( 15) SS BOND : angle 1.08872 ( 30) covalent geometry : bond 0.00289 (10164) covalent geometry : angle 0.58713 (13722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8303 (t0) cc_final: 0.7871 (t0) REVERT: A 159 THR cc_start: 0.8658 (t) cc_final: 0.8387 (p) REVERT: A 168 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: A 213 THR cc_start: 0.9034 (p) cc_final: 0.8815 (t) REVERT: B 120 ASP cc_start: 0.8231 (t0) cc_final: 0.7790 (t0) REVERT: B 121 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7551 (mtp-110) REVERT: B 182 ASP cc_start: 0.8804 (t0) cc_final: 0.8381 (t0) REVERT: B 196 THR cc_start: 0.9018 (m) cc_final: 0.8727 (p) REVERT: B 219 LYS cc_start: 0.8581 (tptp) cc_final: 0.8355 (tptp) REVERT: C 120 ASP cc_start: 0.8311 (t0) cc_final: 0.7814 (t0) REVERT: C 144 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7572 (mtpp) REVERT: C 155 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7793 (mt-10) REVERT: C 159 THR cc_start: 0.8461 (t) cc_final: 0.8140 (p) REVERT: C 219 LYS cc_start: 0.8605 (tptp) cc_final: 0.8335 (tptp) REVERT: SB 25 MET cc_start: 0.8363 (mmm) cc_final: 0.8078 (mmm) REVERT: c 364 ASP cc_start: 0.8926 (m-30) cc_final: 0.8458 (t0) REVERT: c 367 ASP cc_start: 0.8965 (t0) cc_final: 0.8731 (t0) outliers start: 40 outliers final: 18 residues processed: 219 average time/residue: 1.2305 time to fit residues: 288.7532 Evaluate side-chains 202 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain b residue 375 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** SA 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS B 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.077378 restraints weight = 17410.232| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.59 r_work: 0.2738 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10242 Z= 0.262 Angle : 0.700 11.440 13941 Z= 0.343 Chirality : 0.042 0.151 1758 Planarity : 0.004 0.036 1617 Dihedral : 5.893 56.285 2469 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.14 % Allowed : 19.05 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1098 helix: 1.48 (0.23), residues: 531 sheet: 0.20 (0.45), residues: 123 loop : 0.19 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP b 348 HIS 0.004 0.001 HIS A 214 PHE 0.014 0.001 PHE b 402 TYR 0.012 0.002 TYR A 156 ARG 0.006 0.001 ARG b 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 30) link_NAG-ASN : angle 2.21323 ( 90) link_ALPHA1-6 : bond 0.00529 ( 6) link_ALPHA1-6 : angle 1.55563 ( 18) link_BETA1-4 : bond 0.00418 ( 15) link_BETA1-4 : angle 1.59871 ( 45) link_ALPHA1-2 : bond 0.00481 ( 3) link_ALPHA1-2 : angle 1.36584 ( 9) link_ALPHA1-3 : bond 0.00717 ( 6) link_ALPHA1-3 : angle 1.72563 ( 18) hydrogen bonds : bond 0.05138 ( 486) hydrogen bonds : angle 4.94074 ( 1377) link_BETA1-6 : bond 0.00198 ( 3) link_BETA1-6 : angle 1.60122 ( 9) SS BOND : bond 0.00477 ( 15) SS BOND : angle 1.50740 ( 30) covalent geometry : bond 0.00609 (10164) covalent geometry : angle 0.66471 (13722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8558 (t0) cc_final: 0.8072 (t0) REVERT: A 121 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7893 (tpp80) REVERT: A 159 THR cc_start: 0.8728 (t) cc_final: 0.8496 (p) REVERT: A 168 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8234 (mp0) REVERT: A 218 ARG cc_start: 0.8945 (mtp85) cc_final: 0.8734 (mtp85) REVERT: a 268 ASP cc_start: 0.8611 (t70) cc_final: 0.8299 (t0) REVERT: B 120 ASP cc_start: 0.8488 (t0) cc_final: 0.8036 (t0) REVERT: B 121 ARG cc_start: 0.8093 (mtp-110) cc_final: 0.7737 (mtp-110) REVERT: B 144 LYS cc_start: 0.8311 (mmmm) cc_final: 0.7869 (mtpp) REVERT: B 182 ASP cc_start: 0.8934 (t0) cc_final: 0.8572 (t0) REVERT: B 196 THR cc_start: 0.9076 (m) cc_final: 0.8829 (p) REVERT: B 219 LYS cc_start: 0.8685 (tptp) cc_final: 0.8434 (tptp) REVERT: C 120 ASP cc_start: 0.8583 (t0) cc_final: 0.8055 (t0) REVERT: C 144 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7619 (mtpp) REVERT: C 159 THR cc_start: 0.8572 (t) cc_final: 0.8271 (p) REVERT: SB 25 MET cc_start: 0.8499 (mmm) cc_final: 0.8237 (mmm) REVERT: b 268 ASP cc_start: 0.8698 (t70) cc_final: 0.8362 (t0) REVERT: c 268 ASP cc_start: 0.8579 (t70) cc_final: 0.8263 (t0) outliers start: 33 outliers final: 19 residues processed: 198 average time/residue: 1.2952 time to fit residues: 274.2107 Evaluate side-chains 191 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 144 LYS Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 264 ASN B 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.118230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.078880 restraints weight = 17259.010| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.57 r_work: 0.2775 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10242 Z= 0.179 Angle : 0.656 12.305 13941 Z= 0.322 Chirality : 0.041 0.181 1758 Planarity : 0.004 0.041 1617 Dihedral : 5.784 54.185 2469 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.76 % Allowed : 20.57 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.26), residues: 1098 helix: 1.60 (0.23), residues: 531 sheet: 0.24 (0.46), residues: 123 loop : 0.22 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 226 HIS 0.003 0.000 HIS B 199 PHE 0.009 0.001 PHE c 361 TYR 0.012 0.001 TYR b 403 ARG 0.006 0.001 ARG b 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 30) link_NAG-ASN : angle 2.06491 ( 90) link_ALPHA1-6 : bond 0.00588 ( 6) link_ALPHA1-6 : angle 1.55486 ( 18) link_BETA1-4 : bond 0.00375 ( 15) link_BETA1-4 : angle 1.45269 ( 45) link_ALPHA1-2 : bond 0.00551 ( 3) link_ALPHA1-2 : angle 1.28383 ( 9) link_ALPHA1-3 : bond 0.00771 ( 6) link_ALPHA1-3 : angle 1.53831 ( 18) hydrogen bonds : bond 0.04737 ( 486) hydrogen bonds : angle 4.79818 ( 1377) link_BETA1-6 : bond 0.00049 ( 3) link_BETA1-6 : angle 1.46784 ( 9) SS BOND : bond 0.00387 ( 15) SS BOND : angle 1.22764 ( 30) covalent geometry : bond 0.00409 (10164) covalent geometry : angle 0.62427 (13722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8430 (t0) cc_final: 0.7976 (t0) REVERT: A 159 THR cc_start: 0.8749 (t) cc_final: 0.8513 (p) REVERT: A 168 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: A 213 THR cc_start: 0.9043 (p) cc_final: 0.8842 (t) REVERT: A 218 ARG cc_start: 0.8921 (mtp85) cc_final: 0.8676 (mtp85) REVERT: a 268 ASP cc_start: 0.8615 (t70) cc_final: 0.8261 (t0) REVERT: B 120 ASP cc_start: 0.8372 (t0) cc_final: 0.7897 (t0) REVERT: B 121 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7683 (mtp-110) REVERT: B 182 ASP cc_start: 0.8979 (t0) cc_final: 0.8620 (t0) REVERT: B 196 THR cc_start: 0.9077 (m) cc_final: 0.8831 (p) REVERT: B 218 ARG cc_start: 0.8870 (mtm180) cc_final: 0.8596 (mtp-110) REVERT: B 219 LYS cc_start: 0.8680 (tptp) cc_final: 0.8410 (tptp) REVERT: C 120 ASP cc_start: 0.8469 (t0) cc_final: 0.7942 (t0) REVERT: C 144 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7816 (mtpp) REVERT: C 159 THR cc_start: 0.8533 (t) cc_final: 0.8206 (p) REVERT: SB 25 MET cc_start: 0.8497 (mmm) cc_final: 0.8238 (mmm) REVERT: b 268 ASP cc_start: 0.8679 (t70) cc_final: 0.8347 (t0) REVERT: c 268 ASP cc_start: 0.8584 (t70) cc_final: 0.8247 (t0) outliers start: 29 outliers final: 21 residues processed: 204 average time/residue: 1.3764 time to fit residues: 299.3320 Evaluate side-chains 194 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain a residue 255 PHE Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain b residue 375 GLU Chi-restraints excluded: chain c residue 255 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 264 ASN ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN c 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.077082 restraints weight = 17376.730| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.53 r_work: 0.2730 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 10242 Z= 0.248 Angle : 0.713 13.253 13941 Z= 0.349 Chirality : 0.042 0.213 1758 Planarity : 0.004 0.040 1617 Dihedral : 5.933 55.843 2469 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.95 % Allowed : 21.14 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1098 helix: 1.58 (0.23), residues: 528 sheet: 0.19 (0.47), residues: 123 loop : 0.08 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP b 348 HIS 0.004 0.001 HIS A 199 PHE 0.010 0.001 PHE B 127 TYR 0.012 0.002 TYR C 156 ARG 0.007 0.001 ARG a 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 30) link_NAG-ASN : angle 2.17974 ( 90) link_ALPHA1-6 : bond 0.00545 ( 6) link_ALPHA1-6 : angle 1.52248 ( 18) link_BETA1-4 : bond 0.00381 ( 15) link_BETA1-4 : angle 1.55323 ( 45) link_ALPHA1-2 : bond 0.00484 ( 3) link_ALPHA1-2 : angle 1.37728 ( 9) link_ALPHA1-3 : bond 0.00681 ( 6) link_ALPHA1-3 : angle 1.66589 ( 18) hydrogen bonds : bond 0.05144 ( 486) hydrogen bonds : angle 4.93658 ( 1377) link_BETA1-6 : bond 0.00169 ( 3) link_BETA1-6 : angle 1.56663 ( 9) SS BOND : bond 0.00449 ( 15) SS BOND : angle 1.38202 ( 30) covalent geometry : bond 0.00577 (10164) covalent geometry : angle 0.68073 (13722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8694 (t0) cc_final: 0.8351 (t0) REVERT: A 121 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7788 (tpp80) REVERT: A 168 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: A 218 ARG cc_start: 0.8981 (mtp85) cc_final: 0.8752 (mtp85) REVERT: a 268 ASP cc_start: 0.8693 (t70) cc_final: 0.8316 (t0) REVERT: B 120 ASP cc_start: 0.8592 (t0) cc_final: 0.8176 (t0) REVERT: B 182 ASP cc_start: 0.9106 (t0) cc_final: 0.8862 (t0) REVERT: B 196 THR cc_start: 0.9110 (m) cc_final: 0.8862 (p) REVERT: B 219 LYS cc_start: 0.8663 (tptp) cc_final: 0.8390 (tptp) REVERT: C 120 ASP cc_start: 0.8697 (t0) cc_final: 0.8185 (t0) REVERT: C 144 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7868 (mtpp) REVERT: C 159 THR cc_start: 0.8645 (t) cc_final: 0.8352 (p) REVERT: C 193 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7754 (tttp) REVERT: SB 25 MET cc_start: 0.8628 (mmm) cc_final: 0.8398 (mmm) REVERT: b 268 ASP cc_start: 0.8764 (t70) cc_final: 0.8407 (t0) REVERT: c 268 ASP cc_start: 0.8656 (t70) cc_final: 0.8278 (t0) outliers start: 31 outliers final: 17 residues processed: 197 average time/residue: 1.3951 time to fit residues: 293.5214 Evaluate side-chains 185 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 264 ASN ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 34 ASN B 86 GLN B 117 GLN c 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.080291 restraints weight = 17539.332| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.56 r_work: 0.2819 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10242 Z= 0.134 Angle : 0.659 13.415 13941 Z= 0.327 Chirality : 0.040 0.219 1758 Planarity : 0.004 0.045 1617 Dihedral : 5.703 52.771 2469 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.76 % Allowed : 21.52 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.27), residues: 1098 helix: 1.74 (0.23), residues: 528 sheet: -0.03 (0.47), residues: 132 loop : 0.12 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 226 HIS 0.003 0.000 HIS B 199 PHE 0.010 0.001 PHE c 361 TYR 0.011 0.001 TYR C 156 ARG 0.008 0.001 ARG C 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 30) link_NAG-ASN : angle 1.92354 ( 90) link_ALPHA1-6 : bond 0.00624 ( 6) link_ALPHA1-6 : angle 1.53881 ( 18) link_BETA1-4 : bond 0.00402 ( 15) link_BETA1-4 : angle 1.39499 ( 45) link_ALPHA1-2 : bond 0.00573 ( 3) link_ALPHA1-2 : angle 1.25411 ( 9) link_ALPHA1-3 : bond 0.00852 ( 6) link_ALPHA1-3 : angle 1.44461 ( 18) hydrogen bonds : bond 0.04487 ( 486) hydrogen bonds : angle 4.69559 ( 1377) link_BETA1-6 : bond 0.00110 ( 3) link_BETA1-6 : angle 1.37458 ( 9) SS BOND : bond 0.00306 ( 15) SS BOND : angle 1.06162 ( 30) covalent geometry : bond 0.00290 (10164) covalent geometry : angle 0.63219 (13722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8575 (t0) cc_final: 0.8318 (t0) REVERT: A 121 ARG cc_start: 0.8206 (mtp-110) cc_final: 0.7799 (tpp80) REVERT: A 129 GLU cc_start: 0.9160 (tp30) cc_final: 0.8957 (tp30) REVERT: A 168 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: A 213 THR cc_start: 0.9077 (p) cc_final: 0.8866 (t) REVERT: a 268 ASP cc_start: 0.8675 (t70) cc_final: 0.8328 (t0) REVERT: B 120 ASP cc_start: 0.8517 (t0) cc_final: 0.8127 (t0) REVERT: B 121 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7903 (tpp80) REVERT: B 182 ASP cc_start: 0.9071 (t0) cc_final: 0.8752 (t0) REVERT: B 196 THR cc_start: 0.9160 (m) cc_final: 0.8946 (p) REVERT: B 219 LYS cc_start: 0.8658 (tptp) cc_final: 0.8373 (tptp) REVERT: C 120 ASP cc_start: 0.8571 (t0) cc_final: 0.8110 (t0) REVERT: C 144 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7988 (mtpp) REVERT: C 159 THR cc_start: 0.8641 (t) cc_final: 0.8370 (p) REVERT: C 193 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7843 (tttp) REVERT: SB 25 MET cc_start: 0.8590 (mmm) cc_final: 0.8348 (mmm) REVERT: b 268 ASP cc_start: 0.8689 (t70) cc_final: 0.8323 (t0) REVERT: c 268 ASP cc_start: 0.8650 (t70) cc_final: 0.8291 (t0) REVERT: c 364 ASP cc_start: 0.8999 (m-30) cc_final: 0.8645 (t0) outliers start: 29 outliers final: 17 residues processed: 199 average time/residue: 1.4001 time to fit residues: 297.3957 Evaluate side-chains 194 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain a residue 294 SER Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 255 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 43 optimal weight: 0.0870 chunk 57 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 264 ASN B 86 GLN B 117 GLN C 86 GLN c 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.078714 restraints weight = 17541.724| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.59 r_work: 0.2787 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10242 Z= 0.174 Angle : 0.676 13.871 13941 Z= 0.334 Chirality : 0.041 0.219 1758 Planarity : 0.004 0.044 1617 Dihedral : 5.716 54.718 2469 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.29 % Allowed : 22.10 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 1098 helix: 1.75 (0.23), residues: 528 sheet: 0.03 (0.47), residues: 132 loop : 0.08 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 226 HIS 0.004 0.001 HIS A 199 PHE 0.009 0.001 PHE c 361 TYR 0.012 0.001 TYR C 156 ARG 0.007 0.001 ARG b 244 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 30) link_NAG-ASN : angle 1.97364 ( 90) link_ALPHA1-6 : bond 0.00561 ( 6) link_ALPHA1-6 : angle 1.51460 ( 18) link_BETA1-4 : bond 0.00348 ( 15) link_BETA1-4 : angle 1.47702 ( 45) link_ALPHA1-2 : bond 0.00517 ( 3) link_ALPHA1-2 : angle 1.34294 ( 9) link_ALPHA1-3 : bond 0.00727 ( 6) link_ALPHA1-3 : angle 1.54030 ( 18) hydrogen bonds : bond 0.04641 ( 486) hydrogen bonds : angle 4.75590 ( 1377) link_BETA1-6 : bond 0.00021 ( 3) link_BETA1-6 : angle 1.44204 ( 9) SS BOND : bond 0.00361 ( 15) SS BOND : angle 1.23014 ( 30) covalent geometry : bond 0.00398 (10164) covalent geometry : angle 0.64761 (13722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8417.76 seconds wall clock time: 147 minutes 47.87 seconds (8867.87 seconds total)