Starting phenix.real_space_refine on Thu Feb 13 17:02:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fg3_31577/02_2025/7fg3_31577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fg3_31577/02_2025/7fg3_31577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fg3_31577/02_2025/7fg3_31577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fg3_31577/02_2025/7fg3_31577.map" model { file = "/net/cci-nas-00/data/ceres_data/7fg3_31577/02_2025/7fg3_31577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fg3_31577/02_2025/7fg3_31577.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 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 40 5.16 5 C 5750 2.51 5 N 1523 2.21 5 O 1741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9054 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8180 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 49, 'TRANS': 1000} Chain breaks: 4 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Time building chain proxies: 5.54, per 1000 atoms: 0.61 Number of scatterers: 9054 At special positions: 0 Unit cell: (116.604, 110.916, 160.686, 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 40 16.00 O 1741 8.00 N 1523 7.00 C 5750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.21 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 20 sheets defined 19.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 338 through 344 removed outlier: 4.104A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 416 through 422 removed outlier: 4.115A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.036A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 898 through 908 Processing helix chain 'A' and resid 913 through 941 removed outlier: 7.238A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.514A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.661A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.524A pdb=" N ASP D 91 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.559A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.919A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.199A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.106A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.811A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.946A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.016A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.606A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.625A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 644 through 645 removed outlier: 3.654A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 670 through 671 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 721 removed outlier: 3.963A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 721 removed outlier: 3.963A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1063 " --> pdb=" O PHE A1052 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1065 " --> pdb=" O MET A1050 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.132A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A1088 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A1083 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.559A pdb=" N LEU D 19 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.543A pdb=" N THR D 111 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.617A pdb=" N ARG D 39 " --> pdb=" O GLU D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 73 through 74 removed outlier: 3.806A pdb=" N ASP D 74 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR D 79 " --> pdb=" O ASP D 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 244 hydrogen bonds defined for protein. 672 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: 3.38 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2947 1.35 - 1.47: 2314 1.47 - 1.59: 3939 1.59 - 1.72: 2 1.72 - 1.84: 51 Bond restraints: 9253 Sorted by residual: bond pdb=" CA PHE A 833 " pdb=" C PHE A 833 " ideal model delta sigma weight residual 1.524 1.599 -0.076 2.25e-02 1.98e+03 1.14e+01 bond pdb=" CB PRO A 85 " pdb=" CG PRO A 85 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.28e+00 bond pdb=" N CYS A 590 " pdb=" CA CYS A 590 " ideal model delta sigma weight residual 1.455 1.481 -0.026 1.25e-02 6.40e+03 4.31e+00 bond pdb=" CG PRO A1069 " pdb=" CD PRO A1069 " ideal model delta sigma weight residual 1.503 1.434 0.069 3.40e-02 8.65e+02 4.10e+00 bond pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.79e+00 ... (remaining 9248 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 12425 4.03 - 8.07: 143 8.07 - 12.10: 13 12.10 - 16.13: 2 16.13 - 20.16: 1 Bond angle restraints: 12584 Sorted by residual: angle pdb=" CA CYS A 590 " pdb=" C CYS A 590 " pdb=" N SER A 591 " ideal model delta sigma weight residual 117.96 97.80 20.16 1.23e+00 6.61e-01 2.69e+02 angle pdb=" O CYS A 590 " pdb=" C CYS A 590 " pdb=" N SER A 591 " ideal model delta sigma weight residual 122.37 133.26 -10.89 1.28e+00 6.10e-01 7.24e+01 angle pdb=" CA CYS A 590 " pdb=" C CYS A 590 " pdb=" O CYS A 590 " ideal model delta sigma weight residual 119.59 128.94 -9.35 1.23e+00 6.61e-01 5.78e+01 angle pdb=" CA PRO A1069 " pdb=" N PRO A1069 " pdb=" CD PRO A1069 " ideal model delta sigma weight residual 112.00 101.75 10.25 1.40e+00 5.10e-01 5.36e+01 angle pdb=" C CYS A 590 " pdb=" N SER A 591 " pdb=" CA SER A 591 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 ... (remaining 12579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4886 17.32 - 34.65: 494 34.65 - 51.97: 86 51.97 - 69.29: 15 69.29 - 86.61: 12 Dihedral angle restraints: 5493 sinusoidal: 2116 harmonic: 3377 Sorted by residual: dihedral pdb=" CA ASP A 586 " pdb=" C ASP A 586 " pdb=" N ILE A 587 " pdb=" CA ILE A 587 " ideal model delta harmonic sigma weight residual -180.00 -117.60 -62.40 0 5.00e+00 4.00e-02 1.56e+02 dihedral pdb=" CA ASP A 294 " pdb=" C ASP A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta harmonic sigma weight residual 180.00 -118.78 -61.22 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA ASP A 178 " pdb=" C ASP A 178 " pdb=" N LEU A 179 " pdb=" CA LEU A 179 " ideal model delta harmonic sigma weight residual -180.00 -130.97 -49.03 0 5.00e+00 4.00e-02 9.62e+01 ... (remaining 5490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1188 0.073 - 0.146: 209 0.146 - 0.218: 24 0.218 - 0.291: 4 0.291 - 0.364: 2 Chirality restraints: 1427 Sorted by residual: chirality pdb=" CG LEU A 293 " pdb=" CB LEU A 293 " pdb=" CD1 LEU A 293 " pdb=" CD2 LEU A 293 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE A 834 " pdb=" CA ILE A 834 " pdb=" CG1 ILE A 834 " pdb=" CG2 ILE A 834 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA PHE A 592 " pdb=" N PHE A 592 " pdb=" C PHE A 592 " pdb=" CB PHE A 592 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1424 not shown) Planarity restraints: 1636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1068 " -0.095 5.00e-02 4.00e+02 1.37e-01 3.01e+01 pdb=" N PRO A1069 " 0.237 5.00e-02 4.00e+02 pdb=" CA PRO A1069 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A1069 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO A 295 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 449 " 0.030 2.00e-02 2.50e+03 2.83e-02 1.60e+01 pdb=" CG TYR A 449 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 449 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 449 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 449 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 449 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 449 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 449 " 0.003 2.00e-02 2.50e+03 ... (remaining 1633 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 140 2.52 - 3.12: 7832 3.12 - 3.71: 14817 3.71 - 4.31: 20614 4.31 - 4.90: 31670 Nonbonded interactions: 75073 Sorted by model distance: nonbonded pdb=" O TYR A 38 " pdb=" OH TYR A 204 " model vdw 1.929 3.040 nonbonded pdb=" NH1 ARG A 577 " pdb=" OD1 ASP A 578 " model vdw 2.019 3.120 nonbonded pdb=" O ASN A 710 " pdb=" OG1 THR A1077 " model vdw 2.035 3.040 nonbonded pdb=" OE2 GLU A 298 " pdb=" OG1 THR A 315 " model vdw 2.050 3.040 nonbonded pdb=" NE2 GLN A 321 " pdb=" O PRO A 621 " model vdw 2.075 3.120 ... (remaining 75068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.960 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4808 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 0.115 9253 Z= 0.358 Angle : 1.133 20.164 12584 Z= 0.664 Chirality : 0.057 0.364 1427 Planarity : 0.008 0.137 1636 Dihedral : 14.472 86.613 3300 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 37.29 Ramachandran Plot: Outliers : 0.69 % Allowed : 18.54 % Favored : 80.76 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 1.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.21), residues: 1154 helix: -1.71 (0.32), residues: 196 sheet: -2.70 (0.33), residues: 179 loop : -3.79 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 353 HIS 0.006 0.001 HIS A 655 PHE 0.053 0.003 PHE A 898 TYR 0.069 0.003 TYR A 449 ARG 0.011 0.001 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0764 (mmt) cc_final: 0.0560 (mmt) REVERT: A 200 TYR cc_start: 0.3442 (t80) cc_final: 0.2549 (m-80) REVERT: A 204 TYR cc_start: 0.6108 (m-10) cc_final: 0.5800 (m-10) REVERT: A 307 THR cc_start: 0.7545 (m) cc_final: 0.7272 (m) REVERT: A 598 ILE cc_start: 0.3864 (mt) cc_final: 0.3372 (mp) REVERT: A 656 VAL cc_start: 0.7949 (p) cc_final: 0.7404 (t) REVERT: A 951 VAL cc_start: 0.5614 (t) cc_final: 0.5165 (t) REVERT: A 1109 PHE cc_start: 0.5974 (t80) cc_final: 0.5421 (t80) REVERT: D 5 LEU cc_start: 0.6436 (mp) cc_final: 0.6090 (mp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.2045 time to fit residues: 44.7148 Evaluate side-chains 129 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 710 ASN A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.303681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.266621 restraints weight = 17267.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.272043 restraints weight = 11805.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.275687 restraints weight = 8838.374| |-----------------------------------------------------------------------------| r_work (final): 0.5040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4582 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9253 Z= 0.267 Angle : 0.913 15.086 12584 Z= 0.491 Chirality : 0.052 0.258 1427 Planarity : 0.007 0.107 1636 Dihedral : 8.666 65.982 1254 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.69 % Allowed : 16.38 % Favored : 82.93 % Rotamer: Outliers : 1.39 % Allowed : 11.54 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 1.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.22), residues: 1154 helix: -1.27 (0.33), residues: 200 sheet: -2.54 (0.36), residues: 166 loop : -3.51 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.007 0.001 HIS A1088 PHE 0.034 0.002 PHE A 823 TYR 0.027 0.002 TYR A 204 ARG 0.005 0.001 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1120 (mmt) cc_final: 0.0569 (mmt) REVERT: A 200 TYR cc_start: 0.3855 (t80) cc_final: 0.2255 (m-80) REVERT: A 307 THR cc_start: 0.7173 (m) cc_final: 0.6877 (m) REVERT: A 313 TYR cc_start: 0.6181 (m-10) cc_final: 0.5856 (m-10) REVERT: A 656 VAL cc_start: 0.7145 (p) cc_final: 0.6541 (t) REVERT: A 802 PHE cc_start: 0.5859 (m-80) cc_final: 0.5528 (m-80) REVERT: A 1019 ARG cc_start: 0.6980 (ttp-110) cc_final: 0.6724 (ttp-110) REVERT: A 1109 PHE cc_start: 0.5179 (t80) cc_final: 0.4956 (t80) outliers start: 14 outliers final: 8 residues processed: 148 average time/residue: 0.2114 time to fit residues: 43.9298 Evaluate side-chains 129 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 0.0070 chunk 54 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 0.0030 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 954 GLN A 955 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.304752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.266775 restraints weight = 18108.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.272625 restraints weight = 11815.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.274964 restraints weight = 9003.771| |-----------------------------------------------------------------------------| r_work (final): 0.5024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9253 Z= 0.219 Angle : 0.845 14.913 12584 Z= 0.448 Chirality : 0.049 0.268 1427 Planarity : 0.006 0.111 1636 Dihedral : 8.089 65.066 1254 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.78 % Allowed : 14.90 % Favored : 84.32 % Rotamer: Outliers : 2.79 % Allowed : 15.22 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.22), residues: 1154 helix: -1.06 (0.32), residues: 204 sheet: -2.27 (0.38), residues: 173 loop : -3.39 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.006 0.001 HIS A1088 PHE 0.025 0.002 PHE A 541 TYR 0.021 0.002 TYR A 873 ARG 0.009 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.851 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 200 TYR cc_start: 0.3930 (t80) cc_final: 0.1949 (m-80) REVERT: A 275 PHE cc_start: -0.0916 (OUTLIER) cc_final: -0.1322 (m-80) REVERT: A 307 THR cc_start: 0.6937 (m) cc_final: 0.6682 (m) REVERT: A 406 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6570 (tm-30) REVERT: A 598 ILE cc_start: 0.5381 (mt) cc_final: 0.4670 (mp) REVERT: A 616 ASN cc_start: 0.4687 (m-40) cc_final: 0.4392 (m-40) REVERT: A 819 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6342 (mm-30) REVERT: A 1109 PHE cc_start: 0.5218 (t80) cc_final: 0.4911 (t80) outliers start: 28 outliers final: 13 residues processed: 149 average time/residue: 0.2031 time to fit residues: 43.2765 Evaluate side-chains 134 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1036 GLN A1048 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.302053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.263594 restraints weight = 17549.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.269345 restraints weight = 11978.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.272784 restraints weight = 8930.567| |-----------------------------------------------------------------------------| r_work (final): 0.4986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4609 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9253 Z= 0.247 Angle : 0.854 14.668 12584 Z= 0.448 Chirality : 0.050 0.271 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.901 64.836 1254 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.68 % Favored : 83.62 % Rotamer: Outliers : 4.58 % Allowed : 15.22 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.22), residues: 1154 helix: -0.74 (0.33), residues: 206 sheet: -2.29 (0.37), residues: 181 loop : -3.43 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1102 HIS 0.004 0.001 HIS A 207 PHE 0.021 0.002 PHE A 541 TYR 0.023 0.002 TYR A 449 ARG 0.004 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.896 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 307 THR cc_start: 0.6893 (m) cc_final: 0.6662 (m) REVERT: A 321 GLN cc_start: 0.4212 (OUTLIER) cc_final: 0.3961 (tp-100) REVERT: A 338 PHE cc_start: 0.5950 (t80) cc_final: 0.5504 (t80) REVERT: A 402 ILE cc_start: 0.5934 (OUTLIER) cc_final: 0.5409 (tt) REVERT: A 576 VAL cc_start: 0.1441 (OUTLIER) cc_final: 0.1161 (p) REVERT: A 656 VAL cc_start: 0.7471 (p) cc_final: 0.6733 (t) REVERT: A 1095 PHE cc_start: 0.5744 (t80) cc_final: 0.5190 (t80) REVERT: A 1109 PHE cc_start: 0.5434 (t80) cc_final: 0.5081 (t80) REVERT: D 41 ARG cc_start: 0.6673 (mtm110) cc_final: 0.6226 (mtm180) outliers start: 46 outliers final: 23 residues processed: 162 average time/residue: 0.1928 time to fit residues: 44.9302 Evaluate side-chains 146 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 0.0000 chunk 44 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5218 r_free = 0.5218 target = 0.304484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.269048 restraints weight = 18084.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.273799 restraints weight = 12777.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.275587 restraints weight = 9965.484| |-----------------------------------------------------------------------------| r_work (final): 0.4950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4742 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9253 Z= 0.274 Angle : 0.892 14.346 12584 Z= 0.466 Chirality : 0.051 0.309 1427 Planarity : 0.006 0.111 1636 Dihedral : 7.905 64.268 1254 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.90 % Favored : 82.58 % Rotamer: Outliers : 5.37 % Allowed : 16.22 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.22), residues: 1154 helix: -0.85 (0.33), residues: 205 sheet: -2.38 (0.35), residues: 195 loop : -3.45 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS A 655 PHE 0.038 0.002 PHE A 275 TYR 0.020 0.002 TYR A 449 ARG 0.011 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 120 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1132 (OUTLIER) cc_final: 0.0261 (tttm) REVERT: A 307 THR cc_start: 0.6991 (m) cc_final: 0.6742 (m) REVERT: A 406 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7187 (tm-30) REVERT: A 606 ASN cc_start: 0.7092 (t0) cc_final: 0.6508 (t0) REVERT: A 656 VAL cc_start: 0.7509 (p) cc_final: 0.6889 (t) REVERT: A 699 LEU cc_start: 0.4171 (OUTLIER) cc_final: 0.3897 (pp) REVERT: A 712 ILE cc_start: 0.7884 (pt) cc_final: 0.7496 (tp) REVERT: A 1011 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6864 (mm-40) REVERT: A 1095 PHE cc_start: 0.5616 (t80) cc_final: 0.5357 (t80) REVERT: A 1109 PHE cc_start: 0.5712 (t80) cc_final: 0.5321 (t80) REVERT: D 41 ARG cc_start: 0.6668 (mtm110) cc_final: 0.6245 (mtm180) outliers start: 54 outliers final: 23 residues processed: 165 average time/residue: 0.1882 time to fit residues: 44.8456 Evaluate side-chains 141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 0.0370 chunk 104 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 0.0470 chunk 73 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 658 ASN A 928 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.304645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.267846 restraints weight = 18812.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.273725 restraints weight = 12520.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.277839 restraints weight = 9181.420| |-----------------------------------------------------------------------------| r_work (final): 0.4989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4557 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9253 Z= 0.228 Angle : 0.867 16.678 12584 Z= 0.444 Chirality : 0.049 0.262 1427 Planarity : 0.006 0.108 1636 Dihedral : 7.644 63.599 1254 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.90 % Favored : 84.58 % Rotamer: Outliers : 3.58 % Allowed : 17.71 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.23), residues: 1154 helix: -0.69 (0.33), residues: 205 sheet: -2.21 (0.35), residues: 195 loop : -3.37 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.003 0.001 HIS A 655 PHE 0.033 0.002 PHE A 275 TYR 0.037 0.002 TYR A 91 ARG 0.010 0.001 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1012 (OUTLIER) cc_final: 0.0032 (tttm) REVERT: A 307 THR cc_start: 0.7263 (m) cc_final: 0.7039 (m) REVERT: A 606 ASN cc_start: 0.7190 (t0) cc_final: 0.6545 (t0) REVERT: A 656 VAL cc_start: 0.7352 (p) cc_final: 0.6721 (t) REVERT: A 699 LEU cc_start: 0.4907 (OUTLIER) cc_final: 0.4644 (pp) REVERT: A 712 ILE cc_start: 0.7879 (pt) cc_final: 0.7584 (tp) REVERT: A 1109 PHE cc_start: 0.5462 (t80) cc_final: 0.5084 (t80) REVERT: D 41 ARG cc_start: 0.6682 (mtm110) cc_final: 0.6311 (mtm180) outliers start: 36 outliers final: 21 residues processed: 157 average time/residue: 0.1961 time to fit residues: 44.4202 Evaluate side-chains 139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 928 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.303504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.266852 restraints weight = 19362.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.272672 restraints weight = 12847.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4991 r_free = 0.4991 target = 0.276639 restraints weight = 9399.241| |-----------------------------------------------------------------------------| r_work (final): 0.4961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4605 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9253 Z= 0.225 Angle : 0.864 14.552 12584 Z= 0.448 Chirality : 0.050 0.271 1427 Planarity : 0.006 0.109 1636 Dihedral : 7.586 63.101 1254 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.16 % Favored : 84.32 % Rotamer: Outliers : 3.48 % Allowed : 18.51 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.23), residues: 1154 helix: -0.72 (0.33), residues: 207 sheet: -2.24 (0.35), residues: 199 loop : -3.33 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 107 HIS 0.003 0.001 HIS A 655 PHE 0.028 0.002 PHE A 275 TYR 0.040 0.002 TYR A 91 ARG 0.007 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1134 (OUTLIER) cc_final: 0.0095 (tttm) REVERT: A 307 THR cc_start: 0.7032 (m) cc_final: 0.6776 (m) REVERT: A 449 TYR cc_start: 0.3470 (OUTLIER) cc_final: 0.3171 (t80) REVERT: A 606 ASN cc_start: 0.7192 (t0) cc_final: 0.6392 (t0) REVERT: A 643 PHE cc_start: 0.5813 (t80) cc_final: 0.5600 (t80) REVERT: A 656 VAL cc_start: 0.7397 (p) cc_final: 0.6811 (t) REVERT: A 699 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4733 (pp) REVERT: A 712 ILE cc_start: 0.7942 (pt) cc_final: 0.7687 (tp) REVERT: A 734 THR cc_start: 0.7548 (m) cc_final: 0.7168 (m) REVERT: A 900 MET cc_start: 0.1851 (mmp) cc_final: 0.1616 (mmm) REVERT: A 1095 PHE cc_start: 0.4834 (t80) cc_final: 0.4508 (t80) REVERT: A 1109 PHE cc_start: 0.5582 (t80) cc_final: 0.5153 (t80) REVERT: D 41 ARG cc_start: 0.6700 (mtm110) cc_final: 0.6324 (mtm180) outliers start: 35 outliers final: 24 residues processed: 147 average time/residue: 0.1817 time to fit residues: 39.1250 Evaluate side-chains 144 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 935 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 = 0.5178 r_free = 0.5178 target = 0.299360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.272429 restraints weight = 20310.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.269744 restraints weight = 17872.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.272295 restraints weight = 14303.793| |-----------------------------------------------------------------------------| r_work (final): 0.4920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4749 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9253 Z= 0.310 Angle : 0.935 14.565 12584 Z= 0.491 Chirality : 0.054 0.333 1427 Planarity : 0.007 0.111 1636 Dihedral : 7.914 63.514 1254 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.72 % Favored : 82.67 % Rotamer: Outliers : 3.08 % Allowed : 19.40 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.22), residues: 1154 helix: -1.06 (0.33), residues: 208 sheet: -2.48 (0.35), residues: 203 loop : -3.42 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 353 HIS 0.005 0.001 HIS A 655 PHE 0.031 0.003 PHE A 275 TYR 0.022 0.002 TYR A1067 ARG 0.008 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6750 (t80) cc_final: 0.6489 (t80) REVERT: A 182 LYS cc_start: 0.1340 (OUTLIER) cc_final: 0.0210 (tttm) REVERT: A 307 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6853 (m) REVERT: A 449 TYR cc_start: 0.3769 (OUTLIER) cc_final: 0.3490 (t80) REVERT: A 606 ASN cc_start: 0.7099 (t0) cc_final: 0.6268 (t0) REVERT: A 707 TYR cc_start: 0.5247 (t80) cc_final: 0.5045 (m-10) REVERT: A 712 ILE cc_start: 0.7595 (pt) cc_final: 0.7342 (tp) REVERT: A 900 MET cc_start: 0.2269 (mmp) cc_final: 0.1978 (mmm) REVERT: A 1095 PHE cc_start: 0.4806 (t80) cc_final: 0.4536 (t80) REVERT: A 1109 PHE cc_start: 0.5929 (t80) cc_final: 0.5728 (t80) REVERT: D 31 SER cc_start: 0.6418 (OUTLIER) cc_final: 0.5479 (t) REVERT: D 41 ARG cc_start: 0.6607 (mtm110) cc_final: 0.6227 (mtm180) REVERT: D 85 ASN cc_start: 0.5170 (t0) cc_final: 0.4686 (t0) outliers start: 31 outliers final: 21 residues processed: 141 average time/residue: 0.1905 time to fit residues: 39.1141 Evaluate side-chains 139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.1980 chunk 93 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1083 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5197 r_free = 0.5197 target = 0.302606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.270396 restraints weight = 18916.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.272588 restraints weight = 14027.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.275605 restraints weight = 10475.402| |-----------------------------------------------------------------------------| r_work (final): 0.4982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4606 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9253 Z= 0.220 Angle : 0.864 14.738 12584 Z= 0.446 Chirality : 0.050 0.251 1427 Planarity : 0.006 0.108 1636 Dihedral : 7.589 63.188 1254 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.56 % Favored : 84.84 % Rotamer: Outliers : 2.79 % Allowed : 20.70 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.23), residues: 1154 helix: -0.59 (0.34), residues: 203 sheet: -2.35 (0.36), residues: 197 loop : -3.34 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 37 HIS 0.003 0.001 HIS A1058 PHE 0.024 0.002 PHE A 275 TYR 0.027 0.002 TYR A 91 ARG 0.006 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1076 (OUTLIER) cc_final: 0.0036 (tttm) REVERT: A 307 THR cc_start: 0.7244 (m) cc_final: 0.6991 (m) REVERT: A 406 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6865 (tm-30) REVERT: A 449 TYR cc_start: 0.3593 (OUTLIER) cc_final: 0.3325 (t80) REVERT: A 606 ASN cc_start: 0.7609 (t0) cc_final: 0.6965 (t0) REVERT: A 643 PHE cc_start: 0.5841 (t80) cc_final: 0.5630 (t80) REVERT: A 707 TYR cc_start: 0.5139 (t80) cc_final: 0.4924 (m-10) REVERT: A 900 MET cc_start: 0.2335 (mmp) cc_final: 0.2072 (mmm) REVERT: A 938 LEU cc_start: 0.5497 (mp) cc_final: 0.5026 (mp) REVERT: A 1095 PHE cc_start: 0.5111 (t80) cc_final: 0.4816 (t80) REVERT: D 41 ARG cc_start: 0.6746 (mtm110) cc_final: 0.6449 (mtm180) outliers start: 28 outliers final: 22 residues processed: 141 average time/residue: 0.1933 time to fit residues: 39.4491 Evaluate side-chains 134 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 30 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 115 optimal weight: 0.0060 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.303664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.269140 restraints weight = 18977.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.273180 restraints weight = 13812.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.274978 restraints weight = 10850.490| |-----------------------------------------------------------------------------| r_work (final): 0.4965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4636 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9253 Z= 0.220 Angle : 0.880 19.235 12584 Z= 0.450 Chirality : 0.050 0.253 1427 Planarity : 0.006 0.109 1636 Dihedral : 7.438 63.676 1254 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.73 % Favored : 84.66 % Rotamer: Outliers : 2.49 % Allowed : 20.90 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.23), residues: 1154 helix: -0.52 (0.34), residues: 208 sheet: -2.26 (0.36), residues: 197 loop : -3.29 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.003 0.001 HIS A 655 PHE 0.028 0.002 PHE A 906 TYR 0.024 0.002 TYR A 91 ARG 0.006 0.001 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1136 (OUTLIER) cc_final: 0.0109 (tttm) REVERT: A 307 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6953 (m) REVERT: A 449 TYR cc_start: 0.3678 (OUTLIER) cc_final: 0.3226 (t80) REVERT: A 606 ASN cc_start: 0.7640 (t0) cc_final: 0.7070 (t0) REVERT: A 707 TYR cc_start: 0.5047 (t80) cc_final: 0.4847 (m-10) REVERT: A 938 LEU cc_start: 0.5497 (mp) cc_final: 0.5108 (mp) REVERT: A 1095 PHE cc_start: 0.4927 (t80) cc_final: 0.4620 (t80) outliers start: 25 outliers final: 22 residues processed: 136 average time/residue: 0.2037 time to fit residues: 40.0834 Evaluate side-chains 136 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.306556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.280636 restraints weight = 19331.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.279914 restraints weight = 16570.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.283601 restraints weight = 12437.749| |-----------------------------------------------------------------------------| r_work (final): 0.5019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4522 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9253 Z= 0.228 Angle : 0.872 15.269 12584 Z= 0.449 Chirality : 0.050 0.247 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.445 63.498 1254 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.78 % Favored : 85.62 % Rotamer: Outliers : 2.99 % Allowed : 21.59 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.23), residues: 1154 helix: -0.37 (0.35), residues: 208 sheet: -2.24 (0.36), residues: 197 loop : -3.27 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.004 0.001 HIS A 655 PHE 0.023 0.002 PHE A 275 TYR 0.023 0.002 TYR A 91 ARG 0.012 0.001 ARG A 765 =============================================================================== Job complete usr+sys time: 3496.67 seconds wall clock time: 63 minutes 22.81 seconds (3802.81 seconds total)