Starting phenix.real_space_refine on Wed Aug 5 05:24:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfj_71602/08_2026/9pfj_71602.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfj_71602/08_2026/9pfj_71602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pfj_71602/08_2026/9pfj_71602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfj_71602/08_2026/9pfj_71602.map" model { file = "/net/cci-nas-00/data/ceres_data/9pfj_71602/08_2026/9pfj_71602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfj_71602/08_2026/9pfj_71602.cif" } resolution = 3.08 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= 0.007 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 38 5.16 5 C 5270 2.51 5 N 1442 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8378 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2395 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 26, 'TRANS': 279} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 976 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 818 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Restraints were copied for chains: B, C, D Time building chain proxies: 1.74, per 1000 atoms: 0.21 Number of scatterers: 8378 At special positions: 0 Unit cell: (115.275, 81.925, 103.675, 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 38 16.00 O 1628 8.00 N 1442 7.00 C 5270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100E" distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 100E" distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " 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: 0.48 Conformation dependent library (CDL) restraints added in 322.0 milliseconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 20 sheets defined 4.0% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.515A pdb=" N THR H 87 " --> pdb=" O VAL H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.515A pdb=" N THR C 87 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 448 through 450 removed outlier: 4.683A pdb=" N LEU A 249 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 448 through 450 removed outlier: 4.850A pdb=" N VAL A 497 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL A 472 " --> pdb=" O TRP A 520 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TRP A 520 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 474 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 266 removed outlier: 4.583A pdb=" N ARG A 265 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 292 removed outlier: 3.527A pdb=" N THR A 291 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 300 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN A 366 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR A 352 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS A 329 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 389 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 333 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR A 335 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE A 383 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 337 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR A 381 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.621A pdb=" N ASP H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR H 50 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.620A pdb=" N TYR H 100F" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.534A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AB2, first strand: chain 'B' and resid 448 through 450 removed outlier: 4.683A pdb=" N LEU B 249 " --> pdb=" O LEU B 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 448 through 450 removed outlier: 4.849A pdb=" N VAL B 497 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL B 472 " --> pdb=" O TRP B 520 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TRP B 520 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 474 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 265 through 266 removed outlier: 4.582A pdb=" N ARG B 265 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 287 through 292 removed outlier: 3.526A pdb=" N THR B 291 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 300 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN B 366 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TYR B 352 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 329 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 389 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL B 333 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR B 335 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N PHE B 383 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR B 337 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR B 381 " --> pdb=" O THR B 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AB7, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.618A pdb=" N ASP C 58 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 50 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.620A pdb=" N TYR C 100F" --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.534A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'D' and resid 19 through 20 224 hydrogen bonds defined for protein. 546 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: 0.90 Time building geometry restraints manager: 0.70 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: 2755 1.34 - 1.47: 2180 1.47 - 1.59: 3607 1.59 - 1.71: 0 1.71 - 1.84: 54 Bond restraints: 8596 Sorted by residual: bond pdb=" C ARG D 54 " pdb=" N PRO D 55 " ideal model delta sigma weight residual 1.330 1.383 -0.053 1.19e-02 7.06e+03 1.99e+01 bond pdb=" C ARG L 54 " pdb=" N PRO L 55 " ideal model delta sigma weight residual 1.330 1.383 -0.053 1.19e-02 7.06e+03 1.96e+01 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.93e+00 bond pdb=" CB TRP C 47 " pdb=" CG TRP C 47 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.90e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 8591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 10673 1.84 - 3.67: 842 3.67 - 5.51: 175 5.51 - 7.34: 32 7.34 - 9.18: 6 Bond angle restraints: 11728 Sorted by residual: angle pdb=" CA LYS C 43 " pdb=" CB LYS C 43 " pdb=" CG LYS C 43 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" CA LYS H 43 " pdb=" CB LYS H 43 " pdb=" CG LYS H 43 " ideal model delta sigma weight residual 114.10 123.16 -9.06 2.00e+00 2.50e-01 2.05e+01 angle pdb=" C PRO B 529 " pdb=" N MET B 530 " pdb=" CA MET B 530 " ideal model delta sigma weight residual 121.70 128.24 -6.54 1.80e+00 3.09e-01 1.32e+01 angle pdb=" C PRO A 529 " pdb=" N MET A 530 " pdb=" CA MET A 530 " ideal model delta sigma weight residual 121.70 128.21 -6.51 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N TYR B 444 " pdb=" CA TYR B 444 " pdb=" C TYR B 444 " ideal model delta sigma weight residual 112.40 119.82 -7.42 2.07e+00 2.33e-01 1.28e+01 ... (remaining 11723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4497 16.00 - 31.99: 402 31.99 - 47.99: 103 47.99 - 63.98: 48 63.98 - 79.98: 14 Dihedral angle restraints: 5064 sinusoidal: 1958 harmonic: 3106 Sorted by residual: dihedral pdb=" CD ARG B 297 " pdb=" NE ARG B 297 " pdb=" CZ ARG B 297 " pdb=" NH1 ARG B 297 " ideal model delta sinusoidal sigma weight residual 0.00 75.18 -75.18 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CD ARG A 297 " pdb=" NE ARG A 297 " pdb=" CZ ARG A 297 " pdb=" NH1 ARG A 297 " ideal model delta sinusoidal sigma weight residual 0.00 75.16 -75.16 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CD ARG A 435 " pdb=" NE ARG A 435 " pdb=" CZ ARG A 435 " pdb=" NH1 ARG A 435 " ideal model delta sinusoidal sigma weight residual 0.00 -66.11 66.11 1 1.00e+01 1.00e-02 5.71e+01 ... (remaining 5061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 870 0.052 - 0.103: 311 0.103 - 0.154: 89 0.154 - 0.206: 12 0.206 - 0.257: 6 Chirality restraints: 1288 Sorted by residual: chirality pdb=" CA VAL B 499 " pdb=" N VAL B 499 " pdb=" C VAL B 499 " pdb=" CB VAL B 499 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL A 499 " pdb=" N VAL A 499 " pdb=" C VAL A 499 " pdb=" CB VAL A 499 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA TYR B 444 " pdb=" N TYR B 444 " pdb=" C TYR B 444 " pdb=" CB TYR B 444 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1285 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 297 " 0.948 9.50e-02 1.11e+02 4.25e-01 1.15e+02 pdb=" NE ARG A 297 " -0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 297 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 297 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 297 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 297 " 0.947 9.50e-02 1.11e+02 4.25e-01 1.15e+02 pdb=" NE ARG B 297 " -0.072 2.00e-02 2.50e+03 pdb=" CZ ARG B 297 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG B 297 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 297 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 435 " -0.862 9.50e-02 1.11e+02 3.87e-01 1.00e+02 pdb=" NE ARG A 435 " 0.071 2.00e-02 2.50e+03 pdb=" CZ ARG A 435 " -0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG A 435 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 435 " -0.004 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 711 2.74 - 3.28: 8382 3.28 - 3.82: 13417 3.82 - 4.36: 16449 4.36 - 4.90: 29013 Nonbonded interactions: 67972 Sorted by model distance: nonbonded pdb=" NE2 GLN A 430 " pdb=" O HIS A 501 " model vdw 2.199 3.120 nonbonded pdb=" NE2 GLN B 430 " pdb=" O HIS B 501 " model vdw 2.200 3.120 nonbonded pdb=" O GLN B 336 " pdb=" OG1 THR B 344 " model vdw 2.239 3.040 nonbonded pdb=" O GLN A 336 " pdb=" OG1 THR A 344 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP A 370 " pdb=" N THR A 371 " model vdw 2.282 3.120 ... (remaining 67967 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'H' selection = chain 'C' } ncs_group { reference = chain 'L' selection = chain 'D' } 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: 3.380 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.570 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: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 : 0.006 0.064 8602 Z= 0.276 Angle : 1.130 9.179 11740 Z= 0.629 Chirality : 0.058 0.257 1288 Planarity : 0.047 0.425 1546 Dihedral : 15.088 79.979 3070 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.52 % Allowed : 2.81 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1076 helix: -0.03 (1.03), residues: 24 sheet: -0.37 (0.29), residues: 320 loop : -0.42 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.015 ARG L 103 TYR 0.048 0.004 TYR H 50 PHE 0.048 0.005 PHE H 67 TRP 0.018 0.002 TRP B 308 HIS 0.005 0.002 HIS A 492 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.28 ( 8596) covalent geometry : angle 1.12822 / 0.63 (11728) SS BOND : bond 0.00367 / 0.20 ( 6) SS BOND : angle 2.11929 / 1.07 ( 12) hydrogen bonds : bond 0.26550 / 17.54 ( 216) hydrogen bonds : angle 12.23448 / 8.48 ( 546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 0.229 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 247 GLU cc_start: 0.7737 (pp20) cc_final: 0.7491 (pp20) REVERT: A 444 TYR cc_start: 0.8650 (m-80) cc_final: 0.8425 (m-80) REVERT: A 447 MET cc_start: 0.6946 (mtm) cc_final: 0.6726 (mmt) REVERT: B 247 GLU cc_start: 0.7732 (pp20) cc_final: 0.7488 (pp20) REVERT: B 444 TYR cc_start: 0.8655 (m-80) cc_final: 0.8434 (m-80) REVERT: B 447 MET cc_start: 0.6931 (mtm) cc_final: 0.6709 (mmt) outliers start: 14 outliers final: 4 residues processed: 244 average time/residue: 0.0719 time to fit residues: 24.5432 Evaluate side-chains 191 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS A 492 HIS H 82AASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 492 HIS C 82AASN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.132944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116133 restraints weight = 15460.577| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.59 r_work: 0.3784 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8602 Z= 0.154 Angle : 0.708 5.968 11740 Z= 0.385 Chirality : 0.045 0.213 1288 Planarity : 0.007 0.068 1546 Dihedral : 5.987 33.406 1194 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.62 % Allowed : 11.90 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.25), residues: 1076 helix: 1.77 (1.18), residues: 24 sheet: -0.05 (0.28), residues: 346 loop : -0.24 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 94 TYR 0.020 0.002 TYR D 87 PHE 0.015 0.002 PHE A 515 TRP 0.011 0.001 TRP D 35 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 8596) covalent geometry : angle 0.70768 / 0.38 (11728) SS BOND : bond 0.00223 / 0.10 ( 6) SS BOND : angle 1.13290 / 0.71 ( 12) hydrogen bonds : bond 0.05005 / 3.37 ( 216) hydrogen bonds : angle 8.54425 / 5.94 ( 546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.8176 (pp20) cc_final: 0.7745 (pp20) REVERT: A 412 ASN cc_start: 0.9136 (m110) cc_final: 0.8891 (m110) REVERT: H 28 ILE cc_start: 0.8897 (mm) cc_final: 0.8560 (tt) REVERT: L 103 ARG cc_start: 0.8932 (mtp-110) cc_final: 0.8714 (ttm110) REVERT: B 247 GLU cc_start: 0.8182 (pp20) cc_final: 0.7754 (pp20) REVERT: B 412 ASN cc_start: 0.9133 (m110) cc_final: 0.8889 (m110) REVERT: C 28 ILE cc_start: 0.8900 (mm) cc_final: 0.8564 (tt) REVERT: D 103 ARG cc_start: 0.8937 (mtp-110) cc_final: 0.8714 (ttm110) outliers start: 15 outliers final: 11 residues processed: 219 average time/residue: 0.0839 time to fit residues: 25.3882 Evaluate side-chains 191 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 43 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 42 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 ASN A 396 HIS L 34 HIS L 38 GLN B 262 GLN B 309 ASN D 34 HIS D 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.131826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.115393 restraints weight = 15301.154| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.59 r_work: 0.3783 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8602 Z= 0.128 Angle : 0.660 12.345 11740 Z= 0.344 Chirality : 0.043 0.195 1288 Planarity : 0.006 0.050 1546 Dihedral : 5.453 31.311 1188 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.27 % Allowed : 15.58 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.24), residues: 1076 helix: 2.44 (1.22), residues: 24 sheet: -0.28 (0.27), residues: 346 loop : -0.24 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 411 TYR 0.021 0.002 TYR L 87 PHE 0.013 0.002 PHE B 487 TRP 0.010 0.001 TRP D 35 HIS 0.004 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8596) covalent geometry : angle 0.65893 / 0.34 (11728) SS BOND : bond 0.00184 / 0.10 ( 6) SS BOND : angle 1.41481 / 0.82 ( 12) hydrogen bonds : bond 0.04148 / 2.82 ( 216) hydrogen bonds : angle 7.92363 / 5.50 ( 546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.272 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 247 GLU cc_start: 0.8295 (pp20) cc_final: 0.7767 (pp20) REVERT: A 260 GLN cc_start: 0.8565 (tt0) cc_final: 0.8318 (tt0) REVERT: A 412 ASN cc_start: 0.9076 (m110) cc_final: 0.8836 (m110) REVERT: H 28 ILE cc_start: 0.8876 (mm) cc_final: 0.8522 (tt) REVERT: B 247 GLU cc_start: 0.8299 (pp20) cc_final: 0.7771 (pp20) REVERT: B 260 GLN cc_start: 0.8555 (tt0) cc_final: 0.8132 (tt0) REVERT: B 345 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.7752 (mtm-85) REVERT: B 412 ASN cc_start: 0.9067 (m110) cc_final: 0.8830 (m110) REVERT: C 28 ILE cc_start: 0.8881 (mm) cc_final: 0.8528 (tt) outliers start: 21 outliers final: 17 residues processed: 205 average time/residue: 0.0813 time to fit residues: 23.2557 Evaluate side-chains 194 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS A 463 GLN A 479 ASN H 82AASN L 38 GLN B 347 HIS B 430 GLN B 463 GLN B 479 ASN D 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.121276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104457 restraints weight = 16119.932| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.65 r_work: 0.3573 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 8602 Z= 0.247 Angle : 0.743 7.367 11740 Z= 0.391 Chirality : 0.048 0.185 1288 Planarity : 0.006 0.054 1546 Dihedral : 6.114 38.712 1188 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.90 % Allowed : 16.13 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.81 (0.24), residues: 1076 helix: 2.11 (1.22), residues: 24 sheet: -0.70 (0.27), residues: 340 loop : -0.50 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 411 TYR 0.022 0.003 TYR L 36 PHE 0.029 0.003 PHE B 487 TRP 0.018 0.002 TRP C 103 HIS 0.006 0.002 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 ( 8596) covalent geometry : angle 0.74180 / 0.39 (11728) SS BOND : bond 0.00247 / 0.15 ( 6) SS BOND : angle 1.48644 / 0.85 ( 12) hydrogen bonds : bond 0.04061 / 2.69 ( 216) hydrogen bonds : angle 7.77537 / 5.33 ( 546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8543 (tt0) cc_final: 0.8283 (tt0) REVERT: A 412 ASN cc_start: 0.9132 (m110) cc_final: 0.8891 (m110) REVERT: H 28 ILE cc_start: 0.8926 (mm) cc_final: 0.8519 (tt) REVERT: B 260 GLN cc_start: 0.8535 (tt0) cc_final: 0.8277 (tt0) REVERT: B 412 ASN cc_start: 0.9129 (m110) cc_final: 0.8889 (m110) REVERT: C 28 ILE cc_start: 0.8914 (mm) cc_final: 0.8510 (tt) REVERT: D 103 ARG cc_start: 0.8933 (mtp-110) cc_final: 0.8520 (ttm-80) outliers start: 36 outliers final: 29 residues processed: 190 average time/residue: 0.0782 time to fit residues: 20.8676 Evaluate side-chains 191 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN L 38 GLN C 82AASN D 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.125266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.108544 restraints weight = 15760.214| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.61 r_work: 0.3651 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8602 Z= 0.137 Angle : 0.630 6.931 11740 Z= 0.331 Chirality : 0.043 0.168 1288 Planarity : 0.005 0.049 1546 Dihedral : 5.597 35.640 1188 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.49 % Allowed : 18.29 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1076 helix: 2.51 (1.22), residues: 24 sheet: -0.68 (0.27), residues: 340 loop : -0.37 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 94 TYR 0.019 0.002 TYR B 444 PHE 0.038 0.002 PHE B 487 TRP 0.007 0.001 TRP C 103 HIS 0.003 0.001 HIS B 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 8596) covalent geometry : angle 0.62956 / 0.33 (11728) SS BOND : bond 0.00524 / 0.33 ( 6) SS BOND : angle 1.11826 / 0.65 ( 12) hydrogen bonds : bond 0.03581 / 2.40 ( 216) hydrogen bonds : angle 7.24490 / 4.96 ( 546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8385 (tt0) cc_final: 0.7909 (tt0) REVERT: A 488 GLU cc_start: 0.6933 (pp20) cc_final: 0.6619 (pm20) REVERT: H 28 ILE cc_start: 0.8886 (mm) cc_final: 0.8470 (tt) REVERT: H 85 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6955 (pm20) REVERT: L 17 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 260 GLN cc_start: 0.8370 (tt0) cc_final: 0.7920 (tt0) REVERT: B 345 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.7755 (mtm-85) REVERT: B 488 GLU cc_start: 0.6932 (pp20) cc_final: 0.6620 (pm20) REVERT: C 28 ILE cc_start: 0.8890 (mm) cc_final: 0.8477 (tt) REVERT: C 85 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6997 (pm20) REVERT: D 17 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7644 (tm-30) outliers start: 23 outliers final: 20 residues processed: 195 average time/residue: 0.0672 time to fit residues: 18.6532 Evaluate side-chains 192 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.124804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.108219 restraints weight = 15706.625| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.60 r_work: 0.3666 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8602 Z= 0.138 Angle : 0.616 6.536 11740 Z= 0.322 Chirality : 0.043 0.159 1288 Planarity : 0.005 0.047 1546 Dihedral : 5.365 34.023 1188 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.46 % Allowed : 17.75 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1076 helix: 2.51 (1.21), residues: 24 sheet: -0.63 (0.27), residues: 334 loop : -0.47 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 411 TYR 0.017 0.002 TYR A 444 PHE 0.030 0.002 PHE B 487 TRP 0.007 0.001 TRP D 35 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8596) covalent geometry : angle 0.61507 / 0.32 (11728) SS BOND : bond 0.00290 / 0.18 ( 6) SS BOND : angle 1.14846 / 0.66 ( 12) hydrogen bonds : bond 0.03534 / 2.35 ( 216) hydrogen bonds : angle 7.01100 / 4.80 ( 546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 GLN cc_start: 0.8303 (tt0) cc_final: 0.7824 (tt0) REVERT: A 438 MET cc_start: 0.7817 (mmt) cc_final: 0.7517 (mmt) REVERT: H 28 ILE cc_start: 0.8833 (mm) cc_final: 0.8399 (tt) REVERT: H 43 LYS cc_start: 0.4473 (tptp) cc_final: 0.2732 (ttpt) REVERT: H 82 SER cc_start: 0.8842 (m) cc_final: 0.8541 (t) REVERT: H 85 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6977 (pm20) REVERT: B 260 GLN cc_start: 0.8317 (tt0) cc_final: 0.7875 (tt0) REVERT: B 345 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.7742 (mtm-85) REVERT: B 438 MET cc_start: 0.7835 (mmt) cc_final: 0.7512 (mmt) REVERT: B 488 GLU cc_start: 0.6931 (pp20) cc_final: 0.6696 (pm20) REVERT: C 28 ILE cc_start: 0.8874 (mm) cc_final: 0.8446 (tt) REVERT: C 43 LYS cc_start: 0.4473 (tptp) cc_final: 0.2741 (ttpt) REVERT: C 82 SER cc_start: 0.8879 (m) cc_final: 0.8576 (t) REVERT: C 85 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7022 (pm20) outliers start: 32 outliers final: 23 residues processed: 201 average time/residue: 0.0778 time to fit residues: 22.1091 Evaluate side-chains 192 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 70 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.121716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.105124 restraints weight = 16172.482| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.65 r_work: 0.3591 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8602 Z= 0.186 Angle : 0.664 7.951 11740 Z= 0.348 Chirality : 0.044 0.162 1288 Planarity : 0.005 0.046 1546 Dihedral : 5.530 35.636 1188 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.25 % Allowed : 19.05 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.76 (0.24), residues: 1076 helix: 2.50 (1.22), residues: 24 sheet: -0.66 (0.27), residues: 324 loop : -0.50 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 411 TYR 0.016 0.002 TYR B 444 PHE 0.027 0.002 PHE B 487 TRP 0.006 0.001 TRP C 103 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 ( 8596) covalent geometry : angle 0.66370 / 0.35 (11728) SS BOND : bond 0.00224 / 0.14 ( 6) SS BOND : angle 1.13317 / 0.65 ( 12) hydrogen bonds : bond 0.03646 / 2.42 ( 216) hydrogen bonds : angle 7.15606 / 4.91 ( 546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.321 Fit side-chains REVERT: A 260 GLN cc_start: 0.8341 (tt0) cc_final: 0.7863 (tt0) REVERT: A 438 MET cc_start: 0.7838 (mmt) cc_final: 0.7542 (mmt) REVERT: H 28 ILE cc_start: 0.8839 (mm) cc_final: 0.8395 (tt) REVERT: H 43 LYS cc_start: 0.4495 (tptp) cc_final: 0.2790 (ttpt) REVERT: H 82 SER cc_start: 0.8879 (m) cc_final: 0.8580 (t) REVERT: H 85 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6952 (pm20) REVERT: L 17 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7837 (tm-30) REVERT: L 103 ARG cc_start: 0.8978 (mtp-110) cc_final: 0.8563 (ttm-80) REVERT: B 260 GLN cc_start: 0.8335 (tt0) cc_final: 0.7869 (tt0) REVERT: B 345 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.7520 (mtm-85) REVERT: B 438 MET cc_start: 0.7828 (mmt) cc_final: 0.7512 (mmt) REVERT: C 28 ILE cc_start: 0.8842 (mm) cc_final: 0.8403 (tt) REVERT: C 43 LYS cc_start: 0.4520 (tptp) cc_final: 0.2817 (ttpt) REVERT: C 85 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6960 (pm20) REVERT: D 17 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7847 (tm-30) REVERT: D 103 ARG cc_start: 0.8979 (mtp-110) cc_final: 0.8553 (ttm-80) outliers start: 30 outliers final: 25 residues processed: 190 average time/residue: 0.0798 time to fit residues: 21.6206 Evaluate side-chains 190 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 0.1980 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.123644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.106997 restraints weight = 15802.475| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.61 r_work: 0.3623 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8602 Z= 0.147 Angle : 0.640 8.885 11740 Z= 0.333 Chirality : 0.043 0.156 1288 Planarity : 0.005 0.046 1546 Dihedral : 5.380 34.081 1188 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.25 % Allowed : 19.05 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.76 (0.24), residues: 1076 helix: 2.47 (1.20), residues: 24 sheet: -0.66 (0.27), residues: 330 loop : -0.49 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 411 TYR 0.018 0.002 TYR A 444 PHE 0.024 0.002 PHE A 242 TRP 0.006 0.001 TRP D 35 HIS 0.003 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 8596) covalent geometry : angle 0.63908 / 0.33 (11728) SS BOND : bond 0.00283 / 0.17 ( 6) SS BOND : angle 1.09353 / 0.64 ( 12) hydrogen bonds : bond 0.03421 / 2.25 ( 216) hydrogen bonds : angle 6.88520 / 4.74 ( 546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.315 Fit side-chains REVERT: A 260 GLN cc_start: 0.8260 (tt0) cc_final: 0.7772 (tt0) REVERT: A 438 MET cc_start: 0.7733 (mmt) cc_final: 0.7442 (mmt) REVERT: H 28 ILE cc_start: 0.8805 (mm) cc_final: 0.8341 (tt) REVERT: H 43 LYS cc_start: 0.4455 (tptp) cc_final: 0.2750 (ttpt) REVERT: H 82 SER cc_start: 0.8906 (m) cc_final: 0.8608 (t) REVERT: H 85 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6838 (pm20) REVERT: L 17 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7841 (tm-30) REVERT: L 103 ARG cc_start: 0.8964 (mtp-110) cc_final: 0.8554 (ttm-80) REVERT: B 260 GLN cc_start: 0.8277 (tt0) cc_final: 0.7806 (tt0) REVERT: B 345 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.7588 (mtm-85) REVERT: B 438 MET cc_start: 0.7714 (mmt) cc_final: 0.7397 (mmt) REVERT: C 28 ILE cc_start: 0.8817 (mm) cc_final: 0.8364 (tt) REVERT: C 43 LYS cc_start: 0.4451 (tptp) cc_final: 0.2756 (ttpt) REVERT: C 82 SER cc_start: 0.8908 (m) cc_final: 0.8612 (t) REVERT: C 85 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6872 (pm20) REVERT: D 17 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7855 (tm-30) REVERT: D 103 ARG cc_start: 0.8963 (mtp-110) cc_final: 0.8545 (ttm-80) outliers start: 30 outliers final: 24 residues processed: 191 average time/residue: 0.0725 time to fit residues: 19.7799 Evaluate side-chains 189 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 99 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 0.0570 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.124335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.107646 restraints weight = 15718.714| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.61 r_work: 0.3633 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8602 Z= 0.142 Angle : 0.638 8.372 11740 Z= 0.332 Chirality : 0.043 0.158 1288 Planarity : 0.005 0.046 1546 Dihedral : 5.269 32.504 1188 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.25 % Allowed : 18.83 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.82 (0.24), residues: 1076 helix: 2.57 (1.19), residues: 24 sheet: -0.70 (0.27), residues: 332 loop : -0.54 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 411 TYR 0.019 0.002 TYR A 444 PHE 0.024 0.002 PHE B 242 TRP 0.008 0.001 TRP D 35 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 ( 8596) covalent geometry : angle 0.63724 / 0.33 (11728) SS BOND : bond 0.00248 / 0.15 ( 6) SS BOND : angle 1.00363 / 0.58 ( 12) hydrogen bonds : bond 0.03337 / 2.20 ( 216) hydrogen bonds : angle 6.75239 / 4.66 ( 546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.192 Fit side-chains REVERT: A 260 GLN cc_start: 0.8253 (tt0) cc_final: 0.7768 (tt0) REVERT: A 438 MET cc_start: 0.7651 (mmt) cc_final: 0.7384 (mmt) REVERT: H 28 ILE cc_start: 0.8798 (mm) cc_final: 0.8337 (tt) REVERT: H 43 LYS cc_start: 0.4407 (tptp) cc_final: 0.2671 (ttpt) REVERT: H 82 SER cc_start: 0.8884 (m) cc_final: 0.8585 (t) REVERT: H 85 GLU cc_start: 0.7341 (mt-10) cc_final: 0.6825 (pm20) REVERT: L 17 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7840 (tm-30) REVERT: L 103 ARG cc_start: 0.8961 (mtp-110) cc_final: 0.8550 (ttm-80) REVERT: B 260 GLN cc_start: 0.8255 (tt0) cc_final: 0.7783 (tt0) REVERT: B 345 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.7536 (mtm-85) REVERT: B 438 MET cc_start: 0.7643 (mmt) cc_final: 0.7357 (mmt) REVERT: C 28 ILE cc_start: 0.8803 (mm) cc_final: 0.8347 (tt) REVERT: C 43 LYS cc_start: 0.4405 (tptp) cc_final: 0.2676 (ttpt) REVERT: C 82 SER cc_start: 0.8900 (m) cc_final: 0.8621 (t) REVERT: C 85 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6835 (pm20) REVERT: D 17 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7849 (tm-30) REVERT: D 103 ARG cc_start: 0.8962 (mtp-110) cc_final: 0.8545 (ttm-80) outliers start: 30 outliers final: 28 residues processed: 188 average time/residue: 0.0717 time to fit residues: 19.2027 Evaluate side-chains 193 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 99 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN B 504 GLN C 82AASN D 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.120796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.104115 restraints weight = 16110.754| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.63 r_work: 0.3574 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8602 Z= 0.216 Angle : 0.690 8.663 11740 Z= 0.362 Chirality : 0.045 0.161 1288 Planarity : 0.006 0.048 1546 Dihedral : 5.617 35.687 1188 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.57 % Allowed : 18.83 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.24), residues: 1076 helix: 2.13 (1.19), residues: 24 sheet: -0.82 (0.27), residues: 328 loop : -0.65 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 411 TYR 0.020 0.002 TYR A 444 PHE 0.027 0.003 PHE A 487 TRP 0.008 0.002 TRP H 47 HIS 0.005 0.001 HIS L 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 ( 8596) covalent geometry : angle 0.68948 / 0.36 (11728) SS BOND : bond 0.00209 / 0.12 ( 6) SS BOND : angle 1.06083 / 0.61 ( 12) hydrogen bonds : bond 0.03578 / 2.36 ( 216) hydrogen bonds : angle 7.04834 / 4.85 ( 546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.228 Fit side-chains REVERT: A 260 GLN cc_start: 0.8343 (tt0) cc_final: 0.7860 (tt0) REVERT: A 348 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8188 (ttmm) REVERT: A 438 MET cc_start: 0.7726 (mmt) cc_final: 0.7452 (mmt) REVERT: H 28 ILE cc_start: 0.8820 (mm) cc_final: 0.8345 (tt) REVERT: H 43 LYS cc_start: 0.4150 (tptp) cc_final: 0.2510 (ttpt) REVERT: H 85 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6753 (pm20) REVERT: L 17 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7884 (tm-30) REVERT: L 103 ARG cc_start: 0.8975 (mtp-110) cc_final: 0.8562 (ttm-80) REVERT: B 260 GLN cc_start: 0.8329 (tt0) cc_final: 0.7859 (tt0) REVERT: B 345 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.7371 (mtm-85) REVERT: B 438 MET cc_start: 0.7709 (mmt) cc_final: 0.7417 (mmt) REVERT: C 28 ILE cc_start: 0.8827 (mm) cc_final: 0.8363 (tt) REVERT: C 43 LYS cc_start: 0.4304 (tptp) cc_final: 0.2642 (ttpt) REVERT: C 85 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6782 (pm20) REVERT: D 17 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 103 ARG cc_start: 0.8976 (mtp-110) cc_final: 0.8561 (ttm-80) outliers start: 33 outliers final: 30 residues processed: 181 average time/residue: 0.0736 time to fit residues: 18.6426 Evaluate side-chains 188 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 99 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 0.0870 chunk 87 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 GLN ** B 331 GLN ** 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 = 0.4030 r_free = 0.4030 target = 0.124956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.108294 restraints weight = 15687.193| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.61 r_work: 0.3645 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8602 Z= 0.133 Angle : 0.661 9.406 11740 Z= 0.343 Chirality : 0.043 0.159 1288 Planarity : 0.005 0.048 1546 Dihedral : 5.329 32.287 1188 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.71 % Allowed : 20.67 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.85 (0.24), residues: 1076 helix: 2.61 (1.21), residues: 24 sheet: -0.69 (0.27), residues: 328 loop : -0.58 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 411 TYR 0.019 0.002 TYR B 444 PHE 0.023 0.002 PHE B 242 TRP 0.009 0.001 TRP D 35 HIS 0.008 0.001 HIS B 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 8596) covalent geometry : angle 0.66036 / 0.34 (11728) SS BOND : bond 0.00281 / 0.17 ( 6) SS BOND : angle 1.00133 / 0.58 ( 12) hydrogen bonds : bond 0.03269 / 2.15 ( 216) hydrogen bonds : angle 6.73904 / 4.64 ( 546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.26 seconds wall clock time: 33 minutes 9.17 seconds (1989.17 seconds total)