Starting phenix.real_space_refine on Fri Feb 14 05:14:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p4t_17428/02_2025/8p4t_17428.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4t_17428/02_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_17428/02_2025/8p4t_17428.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4t_17428/02_2025/8p4t_17428.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4t_17428/02_2025/8p4t_17428.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4t_17428/02_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-5592/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: 5.43, per 1000 atoms: 0.54 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=5, 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 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: 3.55 Conformation dependent library (CDL) restraints added in 990.0 milliseconds 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: 0.95 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: 2.85 Time building geometry restraints manager: 3.71 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: 5988 13.20 - 26.41: 686 26.41 - 39.61: 223 39.61 - 52.82: 24 52.82 - 66.02: 15 Dihedral angle restraints: 6936 sinusoidal: 3603 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 A 89 " pdb=" SG CYS A 89 " pdb=" SG CYS A 195 " pdb=" CB CYS A 195 " ideal model delta sinusoidal sigma weight residual 93.00 60.44 32.56 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB LYS A 216 " pdb=" CG LYS A 216 " pdb=" CD LYS A 216 " pdb=" CE LYS A 216 " ideal model delta sinusoidal sigma weight residual -60.00 -113.37 53.37 3 1.50e+01 4.44e-03 9.20e+00 ... (remaining 6933 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: 2.03 - 2.60: 71 2.60 - 3.18: 8263 3.18 - 3.75: 15412 3.75 - 4.33: 21986 4.33 - 4.90: 34923 Nonbonded interactions: 80655 Sorted by model distance: nonbonded pdb=" SG CYS c 326 " pdb=" SG CYS c 347 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS b 326 " pdb=" SG CYS b 347 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS b 241 " pdb=" SG CYS b 254 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS c 241 " pdb=" SG CYS c 254 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS C 111 " pdb=" SG CYS C 145 " model vdw 2.031 3.760 ... (remaining 80650 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: 0.700 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.700 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 38.040 ------------------------------------------------------------------------------- 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 10164 Z= 0.160 Angle : 0.542 6.116 13722 Z= 0.298 Chirality : 0.040 0.193 1758 Planarity : 0.003 0.024 1617 Dihedral : 11.922 66.024 4731 Min Nonbonded Distance : 2.027 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 *********************** 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 : 1.205 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: 1.3334 time to fit residues: 467.4878 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 : 1.208 ------------------------------------------------------------------------------- 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: 3.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 281 ASN B 86 GLN SC 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.120812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.081359 restraints weight = 17400.516| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.60 r_work: 0.2838 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10164 Z= 0.356 Angle : 0.655 6.411 13722 Z= 0.344 Chirality : 0.044 0.194 1758 Planarity : 0.004 0.045 1617 Dihedral : 6.803 158.508 2474 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.90 % Allowed : 12.29 % Favored : 83.81 % 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: 0.97 (0.25), residues: 1098 helix: 1.15 (0.22), residues: 513 sheet: 0.54 (0.54), residues: 81 loop : 0.28 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP b 348 HIS 0.007 0.001 HIS B 199 PHE 0.027 0.002 PHE a 402 TYR 0.019 0.002 TYR C 156 ARG 0.006 0.001 ARG c 244 *********************** 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 266 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.122 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: A 120 ASP cc_start: 0.7975 (t0) cc_final: 0.7721 (t0) REVERT: A 159 THR cc_start: 0.8684 (t) cc_final: 0.8431 (t) REVERT: A 182 ASP cc_start: 0.8987 (t0) cc_final: 0.8530 (t0) REVERT: A 218 ARG cc_start: 0.8843 (mtp85) cc_final: 0.8579 (mtp85) REVERT: B 120 ASP cc_start: 0.8067 (t0) cc_final: 0.7838 (t0) REVERT: B 183 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7040 (mmp80) REVERT: B 196 THR cc_start: 0.8911 (m) cc_final: 0.8672 (p) REVERT: C 120 ASP cc_start: 0.8078 (t0) cc_final: 0.7827 (t0) REVERT: C 155 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7753 (mt-10) REVERT: C 168 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: C 182 ASP cc_start: 0.9135 (t0) cc_final: 0.8693 (t0) outliers start: 41 outliers final: 18 residues processed: 242 average time/residue: 1.3376 time to fit residues: 345.2807 Evaluate side-chains 203 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 168 GLU 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 160 LYS 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: 5.9990 chunk 75 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.120528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.081318 restraints weight = 17361.315| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.65 r_work: 0.2863 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10164 Z= 0.220 Angle : 0.589 7.390 13722 Z= 0.308 Chirality : 0.041 0.185 1758 Planarity : 0.004 0.035 1617 Dihedral : 5.701 51.663 2469 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.52 % Allowed : 14.76 % 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: 1.09 (0.25), residues: 1098 helix: 1.25 (0.22), residues: 528 sheet: 0.89 (0.53), residues: 81 loop : 0.24 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 348 HIS 0.004 0.000 HIS B 199 PHE 0.022 0.001 PHE b 402 TYR 0.013 0.001 TYR C 156 ARG 0.008 0.000 ARG A 183 *********************** 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: 37 poor density : 199 time to evaluate : 1.089 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: A 120 ASP cc_start: 0.8087 (t0) cc_final: 0.7721 (t0) REVERT: A 182 ASP cc_start: 0.9078 (t0) cc_final: 0.8568 (t0) REVERT: A 218 ARG cc_start: 0.8898 (mtp85) cc_final: 0.8229 (mtp85) REVERT: A 219 LYS cc_start: 0.8628 (tptp) cc_final: 0.8350 (tptp) REVERT: B 74 MET cc_start: 0.9098 (mmt) cc_final: 0.8780 (mmt) REVERT: B 120 ASP cc_start: 0.8154 (t0) cc_final: 0.7820 (t0) REVERT: B 196 THR cc_start: 0.9107 (m) cc_final: 0.8856 (p) REVERT: B 218 ARG cc_start: 0.8866 (mtm180) cc_final: 0.8526 (mtm180) REVERT: B 219 LYS cc_start: 0.8611 (tptp) cc_final: 0.8312 (tptp) REVERT: C 120 ASP cc_start: 0.8118 (t0) cc_final: 0.7759 (t0) REVERT: C 145 CYS cc_start: 0.9002 (m) cc_final: 0.8360 (m) REVERT: C 155 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7757 (mt-10) REVERT: C 168 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: C 182 ASP cc_start: 0.9091 (t0) cc_final: 0.8687 (t0) REVERT: C 216 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8880 (tttm) REVERT: SB 25 MET cc_start: 0.8362 (mmm) cc_final: 0.8065 (mmm) REVERT: b 241 CYS cc_start: 0.9285 (t) cc_final: 0.8566 (p) REVERT: b 256 ASP cc_start: 0.7047 (p0) cc_final: 0.6779 (p0) outliers start: 37 outliers final: 19 residues processed: 215 average time/residue: 1.1821 time to fit residues: 273.5593 Evaluate side-chains 213 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 a residue 296 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 217 VAL 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 216 LYS 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 c residue 294 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN c 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.080701 restraints weight = 17257.584| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.53 r_work: 0.2833 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10164 Z= 0.276 Angle : 0.594 8.028 13722 Z= 0.309 Chirality : 0.041 0.153 1758 Planarity : 0.004 0.031 1617 Dihedral : 5.785 54.457 2469 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.33 % Allowed : 16.57 % Favored : 80.10 % 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: 1.19 (0.26), residues: 1098 helix: 1.43 (0.23), residues: 528 sheet: 0.14 (0.44), residues: 123 loop : 0.35 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 348 HIS 0.002 0.001 HIS B 199 PHE 0.019 0.001 PHE b 402 TYR 0.013 0.002 TYR C 156 ARG 0.005 0.001 ARG A 183 *********************** 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 236 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8296 (t0) cc_final: 0.7884 (t0) REVERT: A 182 ASP cc_start: 0.9056 (t0) cc_final: 0.8564 (t0) REVERT: A 218 ARG cc_start: 0.8909 (mtp85) cc_final: 0.8693 (mtt-85) REVERT: B 120 ASP cc_start: 0.8268 (t0) cc_final: 0.7890 (t0) REVERT: B 121 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7683 (mtp-110) REVERT: B 145 CYS cc_start: 0.9260 (m) cc_final: 0.8530 (m) REVERT: B 217 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.9049 (m) REVERT: B 218 ARG cc_start: 0.8871 (mtm180) cc_final: 0.8656 (mtm110) REVERT: C 120 ASP cc_start: 0.8272 (t0) cc_final: 0.7868 (t0) REVERT: C 145 CYS cc_start: 0.9058 (m) cc_final: 0.8376 (m) REVERT: C 155 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7785 (mt-10) REVERT: C 168 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: C 182 ASP cc_start: 0.9092 (t0) cc_final: 0.8619 (t0) REVERT: SB 25 MET cc_start: 0.8373 (mmm) cc_final: 0.8099 (mmm) REVERT: b 241 CYS cc_start: 0.9271 (t) cc_final: 0.8368 (p) REVERT: b 256 ASP cc_start: 0.7099 (p0) cc_final: 0.6825 (p0) outliers start: 35 outliers final: 18 residues processed: 216 average time/residue: 1.2729 time to fit residues: 294.5022 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 : 1.131 ------------------------------------------------------------------------------- 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 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 144 LYS 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 SC residue 35 LEU Chi-restraints excluded: chain b residue 350 VAL 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: 1.9990 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS a 264 ASN a 304 ASN B 71 HIS B 86 GLN C 71 HIS C 117 GLN b 304 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.076373 restraints weight = 17432.508| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.59 r_work: 0.2740 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10164 Z= 0.399 Angle : 0.645 9.299 13722 Z= 0.332 Chirality : 0.043 0.143 1758 Planarity : 0.004 0.035 1617 Dihedral : 5.907 54.656 2469 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.81 % Allowed : 17.14 % Favored : 79.05 % 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: 1.12 (0.26), residues: 1098 helix: 1.47 (0.23), residues: 525 sheet: 0.12 (0.45), residues: 123 loop : 0.20 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP b 348 HIS 0.004 0.001 HIS B 199 PHE 0.014 0.001 PHE b 402 TYR 0.012 0.002 TYR C 156 ARG 0.006 0.001 ARG B 183 *********************** 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 223 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.151 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: 0.8431 (t0) cc_final: 0.8115 (t0) REVERT: A 168 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: A 182 ASP cc_start: 0.9128 (t0) cc_final: 0.8639 (t0) REVERT: A 218 ARG cc_start: 0.8982 (mtp85) cc_final: 0.8612 (mtp85) REVERT: B 120 ASP cc_start: 0.8397 (t0) cc_final: 0.7952 (t0) REVERT: B 121 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7639 (mtp-110) REVERT: B 145 CYS cc_start: 0.9223 (m) cc_final: 0.8403 (m) REVERT: B 182 ASP cc_start: 0.9043 (m-30) cc_final: 0.8674 (t0) REVERT: B 217 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8996 (m) REVERT: B 218 ARG cc_start: 0.8819 (mtm180) cc_final: 0.8506 (mtm180) REVERT: B 219 LYS cc_start: 0.8605 (tptp) cc_final: 0.8343 (tptp) REVERT: C 105 LYS cc_start: 0.9296 (ttpt) cc_final: 0.9092 (tttm) REVERT: C 120 ASP cc_start: 0.8479 (t0) cc_final: 0.7971 (t0) REVERT: C 145 CYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8336 (m) REVERT: C 155 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7777 (mt-10) REVERT: C 159 THR cc_start: 0.8494 (m) cc_final: 0.7916 (p) REVERT: C 168 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: C 182 ASP cc_start: 0.9146 (t0) cc_final: 0.8737 (t0) REVERT: SB 25 MET cc_start: 0.8461 (mmm) cc_final: 0.8185 (mmm) outliers start: 40 outliers final: 20 residues processed: 203 average time/residue: 1.3036 time to fit residues: 282.9300 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 : 1.170 ------------------------------------------------------------------------------- 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 127 PHE Chi-restraints excluded: chain B residue 144 LYS 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 145 CYS 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 C residue 221 MET Chi-restraints excluded: chain SB residue 16 ILE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 252 ILE Chi-restraints excluded: chain c residue 254 CYS 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: 1.9990 chunk 30 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN a 264 ASN ** a 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.079647 restraints weight = 17330.308| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.59 r_work: 0.2807 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10164 Z= 0.182 Angle : 0.580 10.483 13722 Z= 0.300 Chirality : 0.040 0.144 1758 Planarity : 0.004 0.040 1617 Dihedral : 5.697 52.288 2469 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.62 % Allowed : 18.29 % Favored : 78.10 % 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: 1.61 (0.23), residues: 528 sheet: 0.26 (0.45), residues: 123 loop : 0.21 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 226 HIS 0.004 0.000 HIS B 199 PHE 0.012 0.001 PHE b 402 TYR 0.013 0.001 TYR C 156 ARG 0.007 0.001 ARG b 244 *********************** 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 235 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8362 (t0) cc_final: 0.7907 (t0) REVERT: A 129 GLU cc_start: 0.9047 (tp30) cc_final: 0.8788 (tp30) REVERT: A 159 THR cc_start: 0.8528 (t) cc_final: 0.8219 (p) REVERT: A 160 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8781 (mtmm) REVERT: A 168 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8195 (mp0) REVERT: A 182 ASP cc_start: 0.9083 (t0) cc_final: 0.8576 (t0) REVERT: A 218 ARG cc_start: 0.8937 (mtp85) cc_final: 0.8539 (mtp85) REVERT: B 120 ASP cc_start: 0.8216 (t0) cc_final: 0.7795 (t0) REVERT: B 121 ARG cc_start: 0.7945 (mtp-110) cc_final: 0.7539 (mtp-110) REVERT: B 145 CYS cc_start: 0.9188 (m) cc_final: 0.8316 (m) REVERT: B 182 ASP cc_start: 0.8999 (m-30) cc_final: 0.8658 (t0) REVERT: B 218 ARG cc_start: 0.8793 (mtm180) cc_final: 0.8475 (mtm180) REVERT: B 219 LYS cc_start: 0.8596 (tptp) cc_final: 0.8290 (tptp) REVERT: C 120 ASP cc_start: 0.8324 (t0) cc_final: 0.7848 (t0) REVERT: C 145 CYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8352 (m) REVERT: C 155 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7746 (mt-10) REVERT: C 168 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: C 182 ASP cc_start: 0.9071 (t0) cc_final: 0.8623 (t0) REVERT: C 216 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8900 (tttm) REVERT: SB 25 MET cc_start: 0.8446 (mmm) cc_final: 0.8169 (mmm) REVERT: b 241 CYS cc_start: 0.9231 (t) cc_final: 0.7859 (p) outliers start: 38 outliers final: 20 residues processed: 216 average time/residue: 1.2908 time to fit residues: 298.2872 Evaluate side-chains 212 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 294 SER Chi-restraints excluded: chain a residue 296 ILE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 144 LYS 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 145 CYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 216 LYS 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 c residue 264 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 43 optimal weight: 0.0570 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- 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 86 GLN C 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 = 0.3595 r_free = 0.3595 target = 0.116655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.077606 restraints weight = 17573.692| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.65 r_work: 0.2765 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10164 Z= 0.278 Angle : 0.612 10.957 13722 Z= 0.313 Chirality : 0.040 0.143 1758 Planarity : 0.004 0.037 1617 Dihedral : 5.736 54.017 2469 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.95 % Allowed : 20.19 % Favored : 76.86 % 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: 1.31 (0.26), residues: 1098 helix: 1.67 (0.23), residues: 528 sheet: 0.25 (0.45), residues: 123 loop : 0.20 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 226 HIS 0.002 0.001 HIS A 214 PHE 0.013 0.001 PHE b 402 TYR 0.013 0.001 TYR C 156 ARG 0.007 0.001 ARG C 218 *********************** 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 220 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.255 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: 0.8426 (t0) cc_final: 0.8086 (t0) REVERT: A 159 THR cc_start: 0.8475 (t) cc_final: 0.8199 (p) REVERT: A 168 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8178 (mp0) REVERT: A 182 ASP cc_start: 0.9108 (t0) cc_final: 0.8703 (t0) REVERT: A 218 ARG cc_start: 0.9007 (mtp85) cc_final: 0.8582 (mtp85) REVERT: B 74 MET cc_start: 0.9072 (mmt) cc_final: 0.8796 (mmt) REVERT: B 120 ASP cc_start: 0.8388 (t0) cc_final: 0.7925 (t0) REVERT: B 121 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.7627 (mtp-110) REVERT: B 145 CYS cc_start: 0.9159 (m) cc_final: 0.8285 (m) REVERT: B 182 ASP cc_start: 0.9057 (m-30) cc_final: 0.8735 (t0) REVERT: B 218 ARG cc_start: 0.8846 (mtm180) cc_final: 0.8495 (mtm110) REVERT: B 219 LYS cc_start: 0.8591 (tptp) cc_final: 0.8262 (tptp) REVERT: C 105 LYS cc_start: 0.9322 (ttpt) cc_final: 0.9084 (tttm) REVERT: C 120 ASP cc_start: 0.8468 (t0) cc_final: 0.7948 (t0) REVERT: C 145 CYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8336 (m) REVERT: C 159 THR cc_start: 0.8543 (t) cc_final: 0.8209 (p) REVERT: C 168 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: C 182 ASP cc_start: 0.9130 (t0) cc_final: 0.8737 (t0) REVERT: SB 25 MET cc_start: 0.8537 (mmm) cc_final: 0.8272 (mmm) outliers start: 31 outliers final: 21 residues processed: 207 average time/residue: 1.3266 time to fit residues: 293.7421 Evaluate side-chains 206 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 76 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 221 MET 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 145 CYS 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 SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 264 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN C 86 GLN C 117 GLN c 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.079194 restraints weight = 17485.441| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.51 r_work: 0.2792 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10164 Z= 0.246 Angle : 0.618 12.273 13722 Z= 0.313 Chirality : 0.040 0.191 1758 Planarity : 0.004 0.040 1617 Dihedral : 5.684 53.274 2469 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.14 % Allowed : 20.86 % Favored : 76.00 % 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 (0.26), residues: 1098 helix: 1.70 (0.23), residues: 528 sheet: -0.18 (0.45), residues: 132 loop : 0.22 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 226 HIS 0.003 0.000 HIS A 199 PHE 0.008 0.001 PHE B 127 TYR 0.013 0.001 TYR C 156 ARG 0.007 0.001 ARG b 244 *********************** 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 215 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8540 (t0) cc_final: 0.8259 (t0) REVERT: A 159 THR cc_start: 0.8670 (t) cc_final: 0.8414 (p) REVERT: A 160 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8808 (mtmm) REVERT: A 168 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: A 182 ASP cc_start: 0.9139 (t0) cc_final: 0.8718 (t0) REVERT: A 218 ARG cc_start: 0.9063 (mtp85) cc_final: 0.8644 (mtp85) REVERT: B 74 MET cc_start: 0.9160 (mmt) cc_final: 0.8863 (mmt) REVERT: B 120 ASP cc_start: 0.8518 (t0) cc_final: 0.8098 (t0) REVERT: B 121 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7790 (mtp-110) REVERT: B 145 CYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8373 (m) REVERT: B 182 ASP cc_start: 0.9047 (m-30) cc_final: 0.8728 (t0) REVERT: B 218 ARG cc_start: 0.8898 (mtm180) cc_final: 0.8584 (mtm110) REVERT: B 219 LYS cc_start: 0.8619 (tptp) cc_final: 0.8289 (tptp) REVERT: C 120 ASP cc_start: 0.8592 (t0) cc_final: 0.8125 (t0) REVERT: C 144 LYS cc_start: 0.8026 (mttt) cc_final: 0.7780 (mtpm) REVERT: C 145 CYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8449 (m) REVERT: C 159 THR cc_start: 0.8646 (t) cc_final: 0.8296 (p) REVERT: C 182 ASP cc_start: 0.9141 (t0) cc_final: 0.8772 (t0) REVERT: C 216 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9063 (tttm) REVERT: SB 25 MET cc_start: 0.8530 (mmm) cc_final: 0.8266 (mmm) outliers start: 33 outliers final: 21 residues processed: 200 average time/residue: 1.2981 time to fit residues: 277.7906 Evaluate side-chains 202 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 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 76 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 221 MET 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 145 CYS Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain SB residue 35 LEU Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 264 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 80 optimal weight: 0.0770 chunk 30 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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** B 86 GLN C 86 GLN c 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078926 restraints weight = 17800.999| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.67 r_work: 0.2792 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10164 Z= 0.233 Angle : 0.617 13.178 13722 Z= 0.313 Chirality : 0.040 0.209 1758 Planarity : 0.004 0.042 1617 Dihedral : 5.653 53.336 2469 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.14 % Allowed : 21.14 % 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: 1.32 (0.26), residues: 1098 helix: 1.77 (0.23), residues: 528 sheet: -0.10 (0.45), residues: 132 loop : 0.20 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 226 HIS 0.003 0.000 HIS A 199 PHE 0.008 0.001 PHE B 127 TYR 0.013 0.001 TYR C 156 ARG 0.008 0.001 ARG a 244 *********************** 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 216 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8549 (t0) cc_final: 0.8272 (t0) REVERT: A 159 THR cc_start: 0.8681 (t) cc_final: 0.8434 (p) REVERT: A 160 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8806 (mtmm) REVERT: A 168 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: A 182 ASP cc_start: 0.9153 (t0) cc_final: 0.8787 (t0) REVERT: A 218 ARG cc_start: 0.9094 (mtp85) cc_final: 0.8695 (mtp85) REVERT: B 74 MET cc_start: 0.9179 (mmt) cc_final: 0.8898 (mmt) REVERT: B 120 ASP cc_start: 0.8498 (t0) cc_final: 0.8087 (t0) REVERT: B 121 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7830 (mtp-110) REVERT: B 145 CYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8348 (m) REVERT: B 182 ASP cc_start: 0.9051 (m-30) cc_final: 0.8748 (t0) REVERT: B 218 ARG cc_start: 0.8917 (mtm180) cc_final: 0.8607 (mtm110) REVERT: C 105 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9133 (tmtm) REVERT: C 120 ASP cc_start: 0.8602 (t0) cc_final: 0.8140 (t0) REVERT: C 145 CYS cc_start: 0.8949 (m) cc_final: 0.8526 (m) REVERT: C 159 THR cc_start: 0.8646 (t) cc_final: 0.8310 (p) REVERT: C 182 ASP cc_start: 0.9138 (t0) cc_final: 0.8783 (t0) REVERT: C 216 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9054 (tttm) REVERT: SB 25 MET cc_start: 0.8583 (mmm) cc_final: 0.8336 (mmm) REVERT: c 268 ASP cc_start: 0.8653 (t70) cc_final: 0.8311 (t0) outliers start: 33 outliers final: 22 residues processed: 204 average time/residue: 1.2924 time to fit residues: 281.9788 Evaluate side-chains 203 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 76 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 145 CYS Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 105 LYS 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 216 LYS Chi-restraints excluded: chain SB residue 35 LEU Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 255 PHE Chi-restraints excluded: chain c residue 264 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** B 86 GLN C 86 GLN c 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.079569 restraints weight = 17537.422| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 3.54 r_work: 0.2805 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10164 Z= 0.223 Angle : 0.621 13.821 13722 Z= 0.315 Chirality : 0.040 0.212 1758 Planarity : 0.004 0.044 1617 Dihedral : 5.603 53.293 2469 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.14 % Allowed : 21.52 % Favored : 75.33 % 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: 1.36 (0.26), residues: 1098 helix: 1.81 (0.23), residues: 528 sheet: -0.03 (0.46), residues: 132 loop : 0.20 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 226 HIS 0.003 0.000 HIS A 199 PHE 0.008 0.001 PHE B 127 TYR 0.014 0.001 TYR C 156 ARG 0.007 0.001 ARG b 244 ********************** 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 216 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8542 (t0) cc_final: 0.8264 (t0) REVERT: A 159 THR cc_start: 0.8675 (t) cc_final: 0.8399 (p) REVERT: A 160 LYS cc_start: 0.9057 (ttmm) cc_final: 0.8797 (mtmm) REVERT: A 168 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8210 (mp0) REVERT: A 182 ASP cc_start: 0.9143 (t0) cc_final: 0.8765 (t0) REVERT: A 218 ARG cc_start: 0.9096 (mtp85) cc_final: 0.8695 (mtp85) REVERT: B 74 MET cc_start: 0.9171 (mmt) cc_final: 0.8885 (mmt) REVERT: B 120 ASP cc_start: 0.8529 (t0) cc_final: 0.8151 (t0) REVERT: B 121 ARG cc_start: 0.8225 (mtp-110) cc_final: 0.7862 (mtp-110) REVERT: B 145 CYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8314 (m) REVERT: B 182 ASP cc_start: 0.9041 (m-30) cc_final: 0.8651 (t0) REVERT: B 218 ARG cc_start: 0.8893 (mtm180) cc_final: 0.8578 (mtm110) REVERT: C 105 LYS cc_start: 0.9374 (tttm) cc_final: 0.9062 (tmtm) REVERT: C 120 ASP cc_start: 0.8590 (t0) cc_final: 0.8134 (t0) REVERT: C 145 CYS cc_start: 0.9034 (m) cc_final: 0.8484 (m) REVERT: C 159 THR cc_start: 0.8610 (t) cc_final: 0.8334 (p) REVERT: C 182 ASP cc_start: 0.9092 (t0) cc_final: 0.8730 (t0) REVERT: SB 25 MET cc_start: 0.8618 (mmm) cc_final: 0.8372 (mmm) REVERT: c 268 ASP cc_start: 0.8650 (t70) cc_final: 0.8293 (t0) outliers start: 33 outliers final: 21 residues processed: 203 average time/residue: 1.3047 time to fit residues: 282.7868 Evaluate side-chains 202 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 a residue 296 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 145 CYS 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 SB residue 35 LEU Chi-restraints excluded: chain SC residue 12 LEU Chi-restraints excluded: chain b residue 255 PHE Chi-restraints excluded: chain b residue 350 VAL Chi-restraints excluded: chain c residue 264 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 0.8980 chunk 16 optimal weight: 0.0470 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- 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** B 86 GLN C 86 GLN b 304 ASN c 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077984 restraints weight = 17745.828| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.57 r_work: 0.2778 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10164 Z= 0.296 Angle : 0.645 13.815 13722 Z= 0.327 Chirality : 0.041 0.227 1758 Planarity : 0.004 0.045 1617 Dihedral : 5.653 54.041 2469 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.67 % Allowed : 22.38 % Favored : 74.95 % 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: 1.39 (0.26), residues: 1098 helix: 1.74 (0.23), residues: 528 sheet: 0.40 (0.47), residues: 123 loop : 0.18 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 226 HIS 0.004 0.001 HIS A 199 PHE 0.009 0.001 PHE B 127 TYR 0.012 0.001 TYR C 156 ARG 0.007 0.001 ARG b 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7316.12 seconds wall clock time: 130 minutes 20.17 seconds (7820.17 seconds total)