Starting phenix.real_space_refine on Wed Jun 3 13:05:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w22_65563/06_2026/9w22_65563.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w22_65563/06_2026/9w22_65563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w22_65563/06_2026/9w22_65563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w22_65563/06_2026/9w22_65563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w22_65563/06_2026/9w22_65563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w22_65563/06_2026/9w22_65563.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3496 2.51 5 N 958 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5532 Number of models: 1 Model: "" Number of chains: 2 Chain: "a" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2766 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Chain: "A" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2766 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Time building chain proxies: 1.45, per 1000 atoms: 0.26 Number of scatterers: 5532 At special positions: 0 Unit cell: (61.061, 93.269, 117.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1036 8.00 N 958 7.00 C 3496 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 315.1 milliseconds 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1284 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 9 sheets defined 20.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'a' and resid 38 through 52 removed outlier: 3.541A pdb=" N GLU a 51 " --> pdb=" O GLN a 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU a 52 " --> pdb=" O LYS a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 Proline residue: a 73 - end of helix Processing helix chain 'a' and resid 114 through 120 removed outlier: 3.617A pdb=" N TRP a 118 " --> pdb=" O SER a 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.585A pdb=" N HIS a 229 " --> pdb=" O PRO a 226 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.632A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.670A pdb=" N TYR a 256 " --> pdb=" O GLN a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.568A pdb=" N LEU a 270 " --> pdb=" O PRO a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.833A pdb=" N ASN a 344 " --> pdb=" O LYS a 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 82 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.628A pdb=" N LEU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.545A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.713A pdb=" N LEU A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 271 " --> pdb=" O TRP A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 271' Processing sheet with id=AA1, first strand: chain 'a' and resid 13 through 17 removed outlier: 3.514A pdb=" N LYS a 14 " --> pdb=" O VAL a 5 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY a 3 " --> pdb=" O GLY a 16 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS a 4 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 4 " --> pdb=" O CYS a 4 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 2 " --> pdb=" O VAL a 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 19 through 22 Processing sheet with id=AA3, first strand: chain 'a' and resid 32 through 36 removed outlier: 3.508A pdb=" N LYS a 33 " --> pdb=" O THR a 165 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 88 through 90 removed outlier: 6.912A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 329 through 331 removed outlier: 4.501A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE a 212 " --> pdb=" O ALA a 205 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA a 205 " --> pdb=" O ILE a 212 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 214 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE A 212 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.372A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.541A pdb=" N TRP A 168 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 157 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS A 170 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL A 155 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.008A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.064A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) 148 hydrogen bonds defined for protein. 390 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: 0.83 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1796 1.35 - 1.47: 1378 1.47 - 1.59: 2442 1.59 - 1.71: 0 1.71 - 1.83: 60 Bond restraints: 5676 Sorted by residual: bond pdb=" CG MET A 123 " pdb=" SD MET A 123 " ideal model delta sigma weight residual 1.803 1.825 -0.022 2.50e-02 1.60e+03 7.76e-01 bond pdb=" CB MET A 123 " pdb=" CG MET A 123 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.18e-01 bond pdb=" CA THR A 72 " pdb=" C THR A 72 " ideal model delta sigma weight residual 1.524 1.533 -0.010 1.26e-02 6.30e+03 5.92e-01 bond pdb=" CB ASP A 197 " pdb=" CG ASP A 197 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.79e-01 bond pdb=" N THR A 72 " pdb=" CA THR A 72 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.41e-02 5.03e+03 5.65e-01 ... (remaining 5671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 7642 2.51 - 5.01: 47 5.01 - 7.52: 2 7.52 - 10.02: 0 10.02 - 12.53: 1 Bond angle restraints: 7692 Sorted by residual: angle pdb=" CB MET A 123 " pdb=" CG MET A 123 " pdb=" SD MET A 123 " ideal model delta sigma weight residual 112.70 125.23 -12.53 3.00e+00 1.11e-01 1.74e+01 angle pdb=" N THR A 72 " pdb=" CA THR A 72 " pdb=" C THR A 72 " ideal model delta sigma weight residual 109.81 116.60 -6.79 2.21e+00 2.05e-01 9.45e+00 angle pdb=" N VAL A 60 " pdb=" CA VAL A 60 " pdb=" C VAL A 60 " ideal model delta sigma weight residual 113.39 108.99 4.40 1.47e+00 4.63e-01 8.95e+00 angle pdb=" CG MET A 123 " pdb=" SD MET A 123 " pdb=" CE MET A 123 " ideal model delta sigma weight residual 100.90 106.28 -5.38 2.20e+00 2.07e-01 5.97e+00 angle pdb=" CA VAL A 60 " pdb=" C VAL A 60 " pdb=" N THR A 61 " ideal model delta sigma weight residual 118.55 116.75 1.80 8.60e-01 1.35e+00 4.36e+00 ... (remaining 7687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 2884 17.49 - 34.97: 396 34.97 - 52.46: 98 52.46 - 69.95: 22 69.95 - 87.43: 8 Dihedral angle restraints: 3408 sinusoidal: 1418 harmonic: 1990 Sorted by residual: dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual -86.00 1.43 -87.43 1 1.00e+01 1.00e-02 9.17e+01 dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 143 " pdb=" CB CYS A 143 " ideal model delta sinusoidal sigma weight residual -86.00 -5.39 -80.61 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS a 313 " pdb=" SG CYS a 313 " pdb=" SG CYS a 316 " pdb=" CB CYS a 316 " ideal model delta sinusoidal sigma weight residual -86.00 -165.69 79.69 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 3405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 533 0.029 - 0.058: 199 0.058 - 0.088: 40 0.088 - 0.117: 41 0.117 - 0.146: 9 Chirality restraints: 822 Sorted by residual: chirality pdb=" CA ILE A 57 " pdb=" N ILE A 57 " pdb=" C ILE A 57 " pdb=" CB ILE A 57 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA THR A 72 " pdb=" N THR A 72 " pdb=" C THR A 72 " pdb=" CB THR A 72 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE A 243 " pdb=" N ILE A 243 " pdb=" C ILE A 243 " pdb=" CB ILE A 243 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 819 not shown) Planarity restraints: 978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP a 208 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ASP a 208 " 0.027 2.00e-02 2.50e+03 pdb=" O ASP a 208 " -0.010 2.00e-02 2.50e+03 pdb=" N THR a 209 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 8 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C TRP A 8 " -0.019 2.00e-02 2.50e+03 pdb=" O TRP A 8 " 0.007 2.00e-02 2.50e+03 pdb=" N LYS A 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 72 " 0.019 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 73 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.016 5.00e-02 4.00e+02 ... (remaining 975 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1747 2.83 - 3.35: 4328 3.35 - 3.86: 8196 3.86 - 4.38: 9463 4.38 - 4.90: 16998 Nonbonded interactions: 40732 Sorted by model distance: nonbonded pdb=" NH1 ARG A 299 " pdb=" OD1 ASP A 327 " model vdw 2.309 3.120 nonbonded pdb=" ND2 ASN a 65 " pdb=" OD2 ASP a 136 " model vdw 2.310 3.120 nonbonded pdb=" O LYS A 85 " pdb=" NZ LYS A 85 " model vdw 2.313 3.120 nonbonded pdb=" NE ARG A 58 " pdb=" OD1 ASN A 145 " model vdw 2.320 3.120 nonbonded pdb=" N ASP a 92 " pdb=" OD1 ASP a 92 " model vdw 2.336 3.120 ... (remaining 40727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } 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: 3.810 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.200 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.003 0.029 5688 Z= 0.123 Angle : 0.507 12.527 7716 Z= 0.267 Chirality : 0.039 0.146 822 Planarity : 0.003 0.033 978 Dihedral : 17.096 87.158 2088 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.45 % Allowed : 27.30 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.32), residues: 688 helix: 2.93 (0.59), residues: 90 sheet: -0.54 (0.46), residues: 142 loop : -1.23 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.012 0.001 TYR A 323 PHE 0.007 0.001 PHE A 279 TRP 0.008 0.001 TRP a 150 HIS 0.001 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 5676) covalent geometry : angle 0.50380 / 0.27 ( 7692) SS BOND : bond 0.00170 / 0.09 ( 12) SS BOND : angle 1.12744 / 0.77 ( 24) hydrogen bonds : bond 0.22918 / 13.70 ( 148) hydrogen bonds : angle 8.08503 / 5.89 ( 390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: a 93 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7251 (pt) REVERT: a 98 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7711 (mp10) REVERT: a 101 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7248 (tptt) REVERT: a 158 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.8047 (t80) REVERT: a 272 ARG cc_start: 0.8576 (ttt180) cc_final: 0.7700 (mtt-85) REVERT: A 14 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6763 (ttpt) REVERT: A 31 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.6230 (pm20) REVERT: A 48 LYS cc_start: 0.8544 (tptt) cc_final: 0.8125 (tptp) REVERT: A 214 LYS cc_start: 0.8671 (pttt) cc_final: 0.8414 (ptpt) REVERT: A 260 TYR cc_start: 0.8470 (m-80) cc_final: 0.7939 (m-80) REVERT: A 288 THR cc_start: 0.8759 (t) cc_final: 0.8418 (p) REVERT: A 329 CYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7594 (t) outliers start: 21 outliers final: 15 residues processed: 87 average time/residue: 0.0709 time to fit residues: 8.2295 Evaluate side-chains 91 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 24 ASN Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 179 CYS Chi-restraints excluded: chain a residue 181 SER Chi-restraints excluded: chain a residue 191 ASN Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 329 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 31 GLN ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.165854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117649 restraints weight = 6312.575| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.15 r_work: 0.3336 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5688 Z= 0.221 Angle : 0.582 7.536 7716 Z= 0.306 Chirality : 0.042 0.160 822 Planarity : 0.004 0.030 978 Dihedral : 7.724 73.412 774 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.76 % Allowed : 22.86 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.32), residues: 688 helix: 2.85 (0.59), residues: 90 sheet: -0.49 (0.41), residues: 182 loop : -1.27 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 299 TYR 0.013 0.002 TYR a 323 PHE 0.010 0.001 PHE a 217 TRP 0.013 0.001 TRP A 311 HIS 0.002 0.001 HIS a 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.22 ( 5676) covalent geometry : angle 0.57691 / 0.30 ( 7692) SS BOND : bond 0.00328 / 0.18 ( 12) SS BOND : angle 1.50902 / 0.98 ( 24) hydrogen bonds : bond 0.05192 / 3.42 ( 148) hydrogen bonds : angle 5.81430 / 4.15 ( 390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.191 Fit side-chains REVERT: a 93 ILE cc_start: 0.7573 (pt) cc_final: 0.7323 (pt) REVERT: a 98 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7510 (mp10) REVERT: a 101 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7197 (tttt) REVERT: a 329 CYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7248 (t) REVERT: A 48 LYS cc_start: 0.8468 (tptt) cc_final: 0.8030 (tptp) REVERT: A 82 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8069 (t0) REVERT: A 94 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7311 (ttpt) REVERT: A 214 LYS cc_start: 0.8593 (pttt) cc_final: 0.8337 (ptpt) REVERT: A 240 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: A 331 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.8201 (m-10) outliers start: 35 outliers final: 23 residues processed: 97 average time/residue: 0.0648 time to fit residues: 8.5520 Evaluate side-chains 92 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 289 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.169639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.123476 restraints weight = 6121.764| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.72 r_work: 0.3395 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5688 Z= 0.098 Angle : 0.486 7.516 7716 Z= 0.252 Chirality : 0.039 0.145 822 Planarity : 0.003 0.026 978 Dihedral : 4.839 39.189 745 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.61 % Allowed : 24.67 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.32), residues: 688 helix: 3.04 (0.58), residues: 90 sheet: -0.34 (0.41), residues: 180 loop : -1.21 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 299 TYR 0.009 0.001 TYR A 323 PHE 0.020 0.001 PHE A 160 TRP 0.008 0.001 TRP a 150 HIS 0.002 0.000 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 5676) covalent geometry : angle 0.48210 / 0.25 ( 7692) SS BOND : bond 0.00165 / 0.10 ( 12) SS BOND : angle 1.15814 / 0.76 ( 24) hydrogen bonds : bond 0.03589 / 2.41 ( 148) hydrogen bonds : angle 5.32653 / 3.78 ( 390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.218 Fit side-chains REVERT: a 93 ILE cc_start: 0.7420 (pt) cc_final: 0.7168 (pt) REVERT: a 98 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7463 (mp10) REVERT: a 101 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7088 (tptt) REVERT: a 158 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.8017 (t80) REVERT: a 274 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: A 31 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6219 (pm20) REVERT: A 48 LYS cc_start: 0.8433 (tptt) cc_final: 0.7965 (tptp) REVERT: A 94 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7288 (ttpt) REVERT: A 214 LYS cc_start: 0.8523 (pttt) cc_final: 0.8267 (ptpt) REVERT: A 260 TYR cc_start: 0.8390 (m-80) cc_final: 0.7815 (m-80) REVERT: A 274 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7925 (mt-10) REVERT: A 288 THR cc_start: 0.8784 (t) cc_final: 0.8435 (p) REVERT: A 293 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7954 (t0) outliers start: 28 outliers final: 15 residues processed: 89 average time/residue: 0.0706 time to fit residues: 8.6206 Evaluate side-chains 83 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 289 GLU Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 9 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN A 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.167772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.121014 restraints weight = 6161.733| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.76 r_work: 0.3348 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5688 Z= 0.153 Angle : 0.530 7.581 7716 Z= 0.275 Chirality : 0.041 0.151 822 Planarity : 0.003 0.025 978 Dihedral : 4.484 37.603 741 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 7.07 % Allowed : 22.20 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.32), residues: 688 helix: 2.98 (0.58), residues: 90 sheet: -0.36 (0.40), residues: 180 loop : -1.28 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 148 TYR 0.011 0.001 TYR a 323 PHE 0.018 0.001 PHE A 160 TRP 0.010 0.001 TRP a 150 HIS 0.003 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 ( 5676) covalent geometry : angle 0.52679 / 0.27 ( 7692) SS BOND : bond 0.00230 / 0.13 ( 12) SS BOND : angle 1.16224 / 0.76 ( 24) hydrogen bonds : bond 0.04028 / 2.72 ( 148) hydrogen bonds : angle 5.23900 / 3.72 ( 390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 65 time to evaluate : 0.211 Fit side-chains REVERT: a 93 ILE cc_start: 0.7527 (pt) cc_final: 0.7281 (pt) REVERT: a 98 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7544 (mp10) REVERT: a 101 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7177 (tttt) REVERT: a 158 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.8048 (t80) REVERT: a 329 CYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7261 (t) REVERT: A 31 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6338 (pm20) REVERT: A 48 LYS cc_start: 0.8455 (tptt) cc_final: 0.8004 (tptp) REVERT: A 94 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7340 (ttpt) REVERT: A 214 LYS cc_start: 0.8568 (pttt) cc_final: 0.8324 (ptpt) REVERT: A 240 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8615 (mt-10) REVERT: A 260 TYR cc_start: 0.8423 (m-80) cc_final: 0.7869 (m-80) REVERT: A 288 THR cc_start: 0.8800 (t) cc_final: 0.8427 (p) REVERT: A 321 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8799 (tp) REVERT: A 331 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.8168 (m-10) outliers start: 43 outliers final: 25 residues processed: 103 average time/residue: 0.0687 time to fit residues: 9.6137 Evaluate side-chains 94 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 289 GLU Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN A 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.169884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122073 restraints weight = 6394.380| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.89 r_work: 0.3350 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5688 Z= 0.148 Angle : 0.529 7.645 7716 Z= 0.273 Chirality : 0.041 0.149 822 Planarity : 0.003 0.025 978 Dihedral : 4.507 38.816 741 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 7.07 % Allowed : 23.03 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.32), residues: 688 helix: 2.99 (0.58), residues: 90 sheet: -0.42 (0.40), residues: 180 loop : -1.29 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.011 0.001 TYR a 323 PHE 0.015 0.001 PHE A 160 TRP 0.009 0.001 TRP a 150 HIS 0.003 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 5676) covalent geometry : angle 0.52460 / 0.27 ( 7692) SS BOND : bond 0.00216 / 0.13 ( 12) SS BOND : angle 1.33353 / 0.91 ( 24) hydrogen bonds : bond 0.03938 / 2.67 ( 148) hydrogen bonds : angle 5.17603 / 3.69 ( 390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 67 time to evaluate : 0.228 Fit side-chains REVERT: a 93 ILE cc_start: 0.7502 (pt) cc_final: 0.7268 (pt) REVERT: a 98 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7521 (mp10) REVERT: a 101 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7167 (tttt) REVERT: a 158 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.8000 (t80) REVERT: a 310 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: a 329 CYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7236 (t) REVERT: A 31 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6324 (pm20) REVERT: A 48 LYS cc_start: 0.8397 (tptt) cc_final: 0.7945 (tptp) REVERT: A 94 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7309 (ttpt) REVERT: A 126 THR cc_start: 0.7596 (OUTLIER) cc_final: 0.7328 (p) REVERT: A 214 LYS cc_start: 0.8553 (pttt) cc_final: 0.8296 (ptpt) REVERT: A 240 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8596 (mt-10) REVERT: A 260 TYR cc_start: 0.8413 (m-80) cc_final: 0.7847 (m-80) REVERT: A 321 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8777 (tp) REVERT: A 331 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.8121 (m-10) outliers start: 43 outliers final: 25 residues processed: 104 average time/residue: 0.0621 time to fit residues: 9.0384 Evaluate side-chains 98 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 289 GLU Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.168407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121726 restraints weight = 6199.983| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.78 r_work: 0.3350 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5688 Z= 0.132 Angle : 0.512 8.233 7716 Z= 0.264 Chirality : 0.040 0.148 822 Planarity : 0.003 0.024 978 Dihedral : 4.250 38.488 739 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.91 % Allowed : 23.19 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.32), residues: 688 helix: 3.00 (0.58), residues: 90 sheet: -0.45 (0.40), residues: 182 loop : -1.26 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.010 0.001 TYR a 323 PHE 0.013 0.001 PHE A 160 TRP 0.009 0.001 TRP a 150 HIS 0.003 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 ( 5676) covalent geometry : angle 0.50824 / 0.26 ( 7692) SS BOND : bond 0.00194 / 0.11 ( 12) SS BOND : angle 1.23687 / 0.84 ( 24) hydrogen bonds : bond 0.03726 / 2.53 ( 148) hydrogen bonds : angle 5.09575 / 3.63 ( 390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 0.229 Fit side-chains REVERT: a 93 ILE cc_start: 0.7515 (pt) cc_final: 0.7287 (pt) REVERT: a 98 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7517 (mp10) REVERT: a 101 LYS cc_start: 0.7843 (mmtt) cc_final: 0.7183 (tttt) REVERT: a 158 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.8039 (t80) REVERT: a 329 CYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7261 (t) REVERT: A 31 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: A 126 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7288 (p) REVERT: A 214 LYS cc_start: 0.8545 (pttt) cc_final: 0.8316 (ptpt) REVERT: A 240 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8596 (mt-10) REVERT: A 288 THR cc_start: 0.8817 (t) cc_final: 0.8475 (p) REVERT: A 321 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8709 (tp) REVERT: A 331 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.8184 (m-10) outliers start: 42 outliers final: 28 residues processed: 107 average time/residue: 0.0635 time to fit residues: 9.3787 Evaluate side-chains 104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 174 ARG Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 185 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 289 GLU Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN A 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.171048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124148 restraints weight = 6372.072| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.81 r_work: 0.3391 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5688 Z= 0.124 Angle : 0.520 8.811 7716 Z= 0.267 Chirality : 0.040 0.146 822 Planarity : 0.003 0.024 978 Dihedral : 4.190 37.591 739 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 7.07 % Allowed : 23.36 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.32), residues: 688 helix: 3.06 (0.58), residues: 90 sheet: -0.34 (0.40), residues: 180 loop : -1.24 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.010 0.001 TYR a 323 PHE 0.012 0.001 PHE A 160 TRP 0.008 0.001 TRP a 150 HIS 0.002 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.12 ( 5676) covalent geometry : angle 0.51650 / 0.27 ( 7692) SS BOND : bond 0.00180 / 0.11 ( 12) SS BOND : angle 1.17851 / 0.81 ( 24) hydrogen bonds : bond 0.03609 / 2.45 ( 148) hydrogen bonds : angle 5.02400 / 3.58 ( 390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 68 time to evaluate : 0.249 Fit side-chains REVERT: a 93 ILE cc_start: 0.7503 (pt) cc_final: 0.7264 (pt) REVERT: a 98 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7519 (mp10) REVERT: a 101 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7169 (tttt) REVERT: a 158 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.8019 (t80) REVERT: a 179 CYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7636 (m) REVERT: a 329 CYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7264 (t) REVERT: A 31 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6335 (pm20) REVERT: A 126 THR cc_start: 0.7573 (OUTLIER) cc_final: 0.7281 (p) REVERT: A 214 LYS cc_start: 0.8535 (pttt) cc_final: 0.8304 (ptpt) REVERT: A 288 THR cc_start: 0.8820 (t) cc_final: 0.8495 (p) REVERT: A 321 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8679 (tp) REVERT: A 331 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.8166 (m-10) outliers start: 43 outliers final: 29 residues processed: 106 average time/residue: 0.0631 time to fit residues: 9.2074 Evaluate side-chains 104 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 174 ARG Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 179 CYS Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 185 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 278 ASP Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 289 GLU Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN A 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.170923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.124812 restraints weight = 6272.610| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.69 r_work: 0.3378 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5688 Z= 0.129 Angle : 0.524 9.141 7716 Z= 0.270 Chirality : 0.040 0.146 822 Planarity : 0.003 0.023 978 Dihedral : 4.189 36.758 739 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 7.57 % Allowed : 22.70 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.32), residues: 688 helix: 3.03 (0.58), residues: 90 sheet: -0.33 (0.40), residues: 180 loop : -1.23 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.010 0.001 TYR a 323 PHE 0.011 0.001 PHE A 160 TRP 0.009 0.001 TRP a 150 HIS 0.002 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 5676) covalent geometry : angle 0.52099 / 0.27 ( 7692) SS BOND : bond 0.00186 / 0.11 ( 12) SS BOND : angle 1.14561 / 0.78 ( 24) hydrogen bonds : bond 0.03619 / 2.45 ( 148) hydrogen bonds : angle 5.02560 / 3.59 ( 390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 70 time to evaluate : 0.233 Fit side-chains REVERT: a 93 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7266 (pt) REVERT: a 98 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7513 (mp10) REVERT: a 101 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7174 (tttt) REVERT: a 158 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.8013 (t80) REVERT: a 179 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7649 (m) REVERT: a 329 CYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7314 (t) REVERT: A 31 GLN cc_start: 0.6627 (OUTLIER) cc_final: 0.6410 (pm20) REVERT: A 48 LYS cc_start: 0.8425 (tptt) cc_final: 0.7953 (tptp) REVERT: A 126 THR cc_start: 0.7583 (OUTLIER) cc_final: 0.7291 (p) REVERT: A 214 LYS cc_start: 0.8542 (pttt) cc_final: 0.8314 (ptpt) REVERT: A 240 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8605 (mt-10) REVERT: A 288 THR cc_start: 0.8818 (t) cc_final: 0.8531 (p) REVERT: A 321 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8684 (tp) REVERT: A 329 CYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7282 (t) REVERT: A 331 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.8175 (m-10) outliers start: 46 outliers final: 31 residues processed: 110 average time/residue: 0.0650 time to fit residues: 9.7971 Evaluate side-chains 110 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 174 ARG Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 179 CYS Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 185 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 289 GLU Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 54 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.169927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124061 restraints weight = 6178.942| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.74 r_work: 0.3378 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5688 Z= 0.124 Angle : 0.513 9.447 7716 Z= 0.265 Chirality : 0.040 0.145 822 Planarity : 0.003 0.024 978 Dihedral : 4.152 35.856 739 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 6.91 % Allowed : 23.68 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.32), residues: 688 helix: 3.04 (0.58), residues: 90 sheet: -0.33 (0.40), residues: 180 loop : -1.22 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.010 0.001 TYR a 323 PHE 0.011 0.001 PHE A 160 TRP 0.009 0.001 TRP a 150 HIS 0.002 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.12 ( 5676) covalent geometry : angle 0.51000 / 0.26 ( 7692) SS BOND : bond 0.00172 / 0.10 ( 12) SS BOND : angle 1.11268 / 0.76 ( 24) hydrogen bonds : bond 0.03545 / 2.41 ( 148) hydrogen bonds : angle 4.98894 / 3.56 ( 390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: a 93 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7284 (pt) REVERT: a 98 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7545 (mp10) REVERT: a 101 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7185 (tttt) REVERT: a 158 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.8015 (t80) REVERT: a 179 CYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7628 (m) REVERT: A 31 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6413 (pm20) REVERT: A 48 LYS cc_start: 0.8415 (tptt) cc_final: 0.7946 (tptp) REVERT: A 94 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7269 (ttpt) REVERT: A 214 LYS cc_start: 0.8549 (pttt) cc_final: 0.8330 (ptpt) REVERT: A 240 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8604 (mt-10) REVERT: A 288 THR cc_start: 0.8832 (t) cc_final: 0.8556 (p) REVERT: A 321 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 329 CYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7300 (t) REVERT: A 331 TYR cc_start: 0.8379 (OUTLIER) cc_final: 0.8178 (m-10) outliers start: 42 outliers final: 32 residues processed: 105 average time/residue: 0.0676 time to fit residues: 9.6086 Evaluate side-chains 111 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 70 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 93 ILE Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 164 THR Chi-restraints excluded: chain a residue 174 ARG Chi-restraints excluded: chain a residue 177 VAL Chi-restraints excluded: chain a residue 179 CYS Chi-restraints excluded: chain a residue 185 SER Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 252 SER Chi-restraints excluded: chain a residue 274 GLU Chi-restraints excluded: chain a residue 278 ASP Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 289 GLU Chi-restraints excluded: chain a residue 301 THR Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 331 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.0170 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.173069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.125268 restraints weight = 6300.064| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.80 r_work: 0.3413 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5688 Z= 0.097 Angle : 0.492 10.322 7716 Z= 0.252 Chirality : 0.039 0.137 822 Planarity : 0.003 0.024 978 Dihedral : 3.909 32.507 739 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 5.43 % Allowed : 25.16 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.32), residues: 688 helix: 3.12 (0.58), residues: 90 sheet: -0.27 (0.40), residues: 180 loop : -1.13 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.009 0.001 TYR A 323 PHE 0.011 0.001 PHE A 160 TRP 0.009 0.001 TRP A 68 HIS 0.002 0.000 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 5676) covalent geometry : angle 0.48931 / 0.25 ( 7692) SS BOND : bond 0.00148 / 0.09 ( 12) SS BOND : angle 1.05863 / 0.73 ( 24) hydrogen bonds : bond 0.03108 / 2.10 ( 148) hydrogen bonds : angle 4.84677 / 3.46 ( 390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: a 93 ILE cc_start: 0.7452 (pt) cc_final: 0.7211 (pt) REVERT: a 98 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7494 (mp10) REVERT: a 101 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7125 (tttt) REVERT: a 158 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.8017 (t80) REVERT: a 179 CYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7532 (m) REVERT: a 274 GLU cc_start: 0.7969 (mp0) cc_final: 0.7671 (mt-10) REVERT: A 31 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.6418 (pm20) REVERT: A 214 LYS cc_start: 0.8498 (pttt) cc_final: 0.8292 (ptpt) REVERT: A 240 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: A 274 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7915 (mt-10) REVERT: A 275 MET cc_start: 0.8985 (ttt) cc_final: 0.8664 (ttt) REVERT: A 288 THR cc_start: 0.8829 (t) cc_final: 0.8570 (p) REVERT: A 321 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8632 (tp) REVERT: A 329 CYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7331 (t) outliers start: 33 outliers final: 22 residues processed: 98 average time/residue: 0.0653 time to fit residues: 8.7641 Evaluate side-chains 96 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 40 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 158 TYR Chi-restraints excluded: chain a residue 174 ARG Chi-restraints excluded: chain a residue 179 CYS Chi-restraints excluded: chain a residue 183 LEU Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 252 SER Chi-restraints excluded: chain a residue 283 THR Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 CYS Chi-restraints excluded: chain a residue 326 GLU Chi-restraints excluded: chain a residue 329 CYS Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.171175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.124632 restraints weight = 6294.486| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.77 r_work: 0.3395 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5688 Z= 0.139 Angle : 0.528 10.986 7716 Z= 0.271 Chirality : 0.040 0.147 822 Planarity : 0.003 0.023 978 Dihedral : 4.034 34.143 737 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.77 % Allowed : 26.48 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.32), residues: 688 helix: 3.11 (0.58), residues: 90 sheet: -0.25 (0.40), residues: 180 loop : -1.19 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 58 TYR 0.011 0.001 TYR a 323 PHE 0.011 0.001 PHE A 160 TRP 0.009 0.001 TRP a 150 HIS 0.002 0.001 HIS a 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 5676) covalent geometry : angle 0.52500 / 0.27 ( 7692) SS BOND : bond 0.00189 / 0.11 ( 12) SS BOND : angle 1.08739 / 0.73 ( 24) hydrogen bonds : bond 0.03634 / 2.46 ( 148) hydrogen bonds : angle 4.96548 / 3.56 ( 390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.62 seconds wall clock time: 28 minutes 33.46 seconds (1713.46 seconds total)