Starting phenix.real_space_refine on Sun Jun 8 02:41:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fg3_31577/06_2025/7fg3_31577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fg3_31577/06_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_31577/06_2025/7fg3_31577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fg3_31577/06_2025/7fg3_31577.map" model { file = "/net/cci-nas-00/data/ceres_data/7fg3_31577/06_2025/7fg3_31577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fg3_31577/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.67, per 1000 atoms: 0.63 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: 2.51 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: 1.06 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: 3.14 Time building geometry restraints manager: 2.86 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: 1.010 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.940 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- 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 0.180 9262 Z= 0.287 Angle : 1.138 20.164 12602 Z= 0.666 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 Details of bonding type rmsd hydrogen bonds : bond 0.24804 ( 237) hydrogen bonds : angle 11.23295 ( 672) SS BOND : bond 0.06015 ( 9) SS BOND : angle 2.97875 ( 18) covalent geometry : bond 0.00559 ( 9253) covalent geometry : angle 1.13302 (12584) *********************** 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 : 1.058 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: 0.2113 time to fit residues: 46.4797 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 : 1.035 ------------------------------------------------------------------------------- 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 = 0.303677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.266733 restraints weight = 17268.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.271985 restraints weight = 11827.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.275713 restraints weight = 8830.455| |-----------------------------------------------------------------------------| r_work (final): 0.5040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4580 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 9262 Z= 0.199 Angle : 0.916 15.088 12602 Z= 0.492 Chirality : 0.052 0.258 1427 Planarity : 0.007 0.107 1636 Dihedral : 8.666 65.982 1254 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.78 % Allowed : 16.20 % Favored : 83.02 % 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 Details of bonding type rmsd hydrogen bonds : bond 0.06667 ( 237) hydrogen bonds : angle 8.21947 ( 672) SS BOND : bond 0.00620 ( 9) SS BOND : angle 2.04494 ( 18) covalent geometry : bond 0.00409 ( 9253) covalent geometry : angle 0.91291 (12584) *********************** 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 : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1111 (mmt) cc_final: 0.0558 (mmt) REVERT: A 200 TYR cc_start: 0.3848 (t80) cc_final: 0.2249 (m-80) REVERT: A 307 THR cc_start: 0.7176 (m) cc_final: 0.6881 (m) REVERT: A 313 TYR cc_start: 0.6178 (m-10) cc_final: 0.5852 (m-10) REVERT: A 656 VAL cc_start: 0.7150 (p) cc_final: 0.6545 (t) REVERT: A 802 PHE cc_start: 0.5863 (m-80) cc_final: 0.5530 (m-80) REVERT: A 1019 ARG cc_start: 0.6973 (ttp-110) cc_final: 0.6718 (ttp-110) REVERT: A 1109 PHE cc_start: 0.5165 (t80) cc_final: 0.4948 (t80) outliers start: 14 outliers final: 8 residues processed: 148 average time/residue: 0.2242 time to fit residues: 46.3444 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 : 1.006 ------------------------------------------------------------------------------- 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: 0.3980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 85 optimal weight: 0.0170 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 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 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5216 r_free = 0.5216 target = 0.304372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.267934 restraints weight = 18525.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.273065 restraints weight = 12779.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.276888 restraints weight = 9634.587| |-----------------------------------------------------------------------------| r_work (final): 0.4995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4580 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9262 Z= 0.177 Angle : 0.859 14.832 12602 Z= 0.456 Chirality : 0.050 0.271 1427 Planarity : 0.006 0.111 1636 Dihedral : 8.134 64.880 1254 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.34 % Favored : 83.97 % Rotamer: Outliers : 2.99 % Allowed : 14.83 % Favored : 82.19 % 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: -4.02 (0.22), residues: 1154 helix: -1.12 (0.32), residues: 204 sheet: -2.40 (0.37), residues: 180 loop : -3.42 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 353 HIS 0.006 0.001 HIS A1088 PHE 0.026 0.002 PHE A 541 TYR 0.021 0.002 TYR A 449 ARG 0.009 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.05737 ( 237) hydrogen bonds : angle 7.35319 ( 672) SS BOND : bond 0.00463 ( 9) SS BOND : angle 1.57377 ( 18) covalent geometry : bond 0.00359 ( 9253) covalent geometry : angle 0.85745 (12584) *********************** 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 160 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.931 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 226 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7442 (mp) REVERT: A 307 THR cc_start: 0.6990 (m) cc_final: 0.6724 (m) REVERT: A 1109 PHE cc_start: 0.5309 (t80) cc_final: 0.5037 (t80) REVERT: D 41 ARG cc_start: 0.6631 (mtm110) cc_final: 0.6157 (mtm180) outliers start: 30 outliers final: 17 residues processed: 153 average time/residue: 0.1954 time to fit residues: 42.8799 Evaluate side-chains 139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU 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 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 VAL 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: 0.5980 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 74 optimal weight: 0.0370 chunk 5 optimal weight: 5.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 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 901 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5207 r_free = 0.5207 target = 0.303949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.265069 restraints weight = 17233.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.271286 restraints weight = 11234.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.275595 restraints weight = 8127.469| |-----------------------------------------------------------------------------| r_work (final): 0.5011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9262 Z= 0.163 Angle : 0.834 14.778 12602 Z= 0.438 Chirality : 0.049 0.261 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.849 65.457 1254 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.42 % Favored : 83.88 % Rotamer: Outliers : 4.38 % Allowed : 15.32 % Favored : 80.30 % 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: -3.85 (0.23), residues: 1154 helix: -0.74 (0.34), residues: 206 sheet: -2.20 (0.38), residues: 176 loop : -3.41 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.004 0.001 HIS A 207 PHE 0.036 0.002 PHE A 275 TYR 0.023 0.001 TYR A 449 ARG 0.004 0.001 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 237) hydrogen bonds : angle 6.99687 ( 672) SS BOND : bond 0.00881 ( 9) SS BOND : angle 1.96149 ( 18) covalent geometry : bond 0.00341 ( 9253) covalent geometry : angle 0.83169 (12584) *********************** 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 174 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.914 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 84 LEU cc_start: 0.4184 (mt) cc_final: 0.3900 (mt) REVERT: A 226 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7346 (mp) REVERT: A 307 THR cc_start: 0.6768 (m) cc_final: 0.6534 (m) REVERT: A 321 GLN cc_start: 0.4055 (OUTLIER) cc_final: 0.3588 (tp-100) REVERT: A 402 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5249 (tt) REVERT: A 576 VAL cc_start: 0.1674 (OUTLIER) cc_final: 0.1422 (p) REVERT: A 656 VAL cc_start: 0.7381 (p) cc_final: 0.6610 (t) REVERT: A 729 VAL cc_start: 0.7331 (m) cc_final: 0.7076 (m) REVERT: A 1109 PHE cc_start: 0.5260 (t80) cc_final: 0.4975 (t80) REVERT: D 41 ARG cc_start: 0.6668 (mtm110) cc_final: 0.6242 (mtm180) outliers start: 44 outliers final: 20 residues processed: 169 average time/residue: 0.1886 time to fit residues: 46.0165 Evaluate side-chains 147 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU 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 321 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 470 THR 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 726 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 906 PHE 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 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: 9.9990 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 954 GLN A1011 GLN ** 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 = 0.5179 r_free = 0.5179 target = 0.299467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.275436 restraints weight = 20518.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.275407 restraints weight = 19641.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.275133 restraints weight = 14033.680| |-----------------------------------------------------------------------------| r_work (final): 0.4934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4775 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 9262 Z= 0.263 Angle : 0.985 14.015 12602 Z= 0.520 Chirality : 0.055 0.299 1427 Planarity : 0.007 0.115 1636 Dihedral : 8.296 64.421 1254 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.61 % Allowed : 18.11 % Favored : 81.28 % Rotamer: Outliers : 5.27 % Allowed : 17.41 % Favored : 77.31 % 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: -4.18 (0.22), residues: 1154 helix: -1.18 (0.32), residues: 205 sheet: -2.53 (0.35), residues: 192 loop : -3.55 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.005 0.002 HIS A 655 PHE 0.032 0.003 PHE A 275 TYR 0.027 0.003 TYR A 91 ARG 0.007 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.06874 ( 237) hydrogen bonds : angle 7.41392 ( 672) SS BOND : bond 0.01129 ( 9) SS BOND : angle 2.77507 ( 18) covalent geometry : bond 0.00557 ( 9253) covalent geometry : angle 0.98018 (12584) *********************** 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 176 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1426 (OUTLIER) cc_final: 0.0465 (tttm) REVERT: A 307 THR cc_start: 0.7309 (m) cc_final: 0.7090 (m) REVERT: A 321 GLN cc_start: 0.5068 (OUTLIER) cc_final: 0.4596 (tp-100) REVERT: A 576 VAL cc_start: 0.1859 (OUTLIER) cc_final: 0.1513 (p) REVERT: A 606 ASN cc_start: 0.7216 (t0) cc_final: 0.6606 (t0) REVERT: A 712 ILE cc_start: 0.7639 (pt) cc_final: 0.7238 (tp) REVERT: A 1095 PHE cc_start: 0.4993 (t80) cc_final: 0.4615 (t80) REVERT: A 1109 PHE cc_start: 0.5803 (t80) cc_final: 0.5588 (t80) REVERT: D 41 ARG cc_start: 0.6565 (mtm110) cc_final: 0.6165 (mtm180) outliers start: 53 outliers final: 25 residues processed: 166 average time/residue: 0.1801 time to fit residues: 43.6117 Evaluate side-chains 142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 469 SER Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 576 VAL 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 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 928 ASN Chi-restraints excluded: chain A residue 1048 HIS Chi-restraints excluded: chain A residue 1060 VAL 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 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: 0.5980 chunk 104 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 658 ASN A1083 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5195 r_free = 0.5195 target = 0.302408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.267067 restraints weight = 18561.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.270721 restraints weight = 13261.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.271943 restraints weight = 11289.995| |-----------------------------------------------------------------------------| r_work (final): 0.4964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4654 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9262 Z= 0.165 Angle : 0.867 14.669 12602 Z= 0.449 Chirality : 0.050 0.256 1427 Planarity : 0.006 0.112 1636 Dihedral : 7.762 63.277 1254 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.64 % Favored : 84.84 % Rotamer: Outliers : 4.08 % Allowed : 18.71 % Favored : 77.21 % 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: -3.99 (0.22), residues: 1154 helix: -0.99 (0.32), residues: 205 sheet: -2.39 (0.35), residues: 194 loop : -3.44 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 107 HIS 0.003 0.001 HIS A 655 PHE 0.024 0.002 PHE A 275 TYR 0.035 0.002 TYR A 380 ARG 0.009 0.001 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.05259 ( 237) hydrogen bonds : angle 6.77040 ( 672) SS BOND : bond 0.00681 ( 9) SS BOND : angle 2.07854 ( 18) covalent geometry : bond 0.00341 ( 9253) covalent geometry : angle 0.86360 (12584) *********************** 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 165 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1024 (OUTLIER) cc_final: 0.0156 (tttm) REVERT: A 307 THR cc_start: 0.7190 (m) cc_final: 0.6957 (m) REVERT: A 321 GLN cc_start: 0.3379 (OUTLIER) cc_final: 0.2824 (tp-100) REVERT: A 576 VAL cc_start: 0.1427 (OUTLIER) cc_final: 0.1108 (p) REVERT: A 606 ASN cc_start: 0.7319 (t0) cc_final: 0.6579 (t0) REVERT: A 616 ASN cc_start: 0.4692 (m-40) cc_final: 0.4204 (m-40) REVERT: A 643 PHE cc_start: 0.5659 (t80) cc_final: 0.5456 (t80) REVERT: A 712 ILE cc_start: 0.7939 (pt) cc_final: 0.7658 (tp) REVERT: A 900 MET cc_start: 0.1819 (mmp) cc_final: 0.1583 (mmm) REVERT: A 1095 PHE cc_start: 0.5084 (t80) cc_final: 0.4666 (t80) REVERT: A 1109 PHE cc_start: 0.5604 (t80) cc_final: 0.5222 (t80) REVERT: D 41 ARG cc_start: 0.6631 (mtm110) cc_final: 0.6229 (mtm180) outliers start: 41 outliers final: 23 residues processed: 159 average time/residue: 0.2035 time to fit residues: 46.4229 Evaluate side-chains 145 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP 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 402 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 576 VAL 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 861 LEU 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 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: 1.9990 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 928 ASN ** D 40 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 = 0.300031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.262430 restraints weight = 18757.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.266715 restraints weight = 14254.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.270517 restraints weight = 9337.510| |-----------------------------------------------------------------------------| r_work (final): 0.4963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4721 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9262 Z= 0.169 Angle : 0.859 14.613 12602 Z= 0.448 Chirality : 0.050 0.250 1427 Planarity : 0.006 0.114 1636 Dihedral : 7.679 63.112 1254 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.29 % Favored : 83.10 % Rotamer: Outliers : 3.48 % Allowed : 20.30 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % 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: -3.91 (0.22), residues: 1154 helix: -0.85 (0.33), residues: 205 sheet: -2.37 (0.35), residues: 204 loop : -3.41 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS A 655 PHE 0.022 0.002 PHE A 275 TYR 0.022 0.002 TYR A 200 ARG 0.008 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 237) hydrogen bonds : angle 6.70678 ( 672) SS BOND : bond 0.00627 ( 9) SS BOND : angle 1.83394 ( 18) covalent geometry : bond 0.00352 ( 9253) covalent geometry : angle 0.85644 (12584) *********************** 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 157 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1115 (OUTLIER) cc_final: 0.0080 (tttm) REVERT: A 275 PHE cc_start: 0.1257 (OUTLIER) cc_final: 0.0879 (m-80) REVERT: A 307 THR cc_start: 0.7231 (m) cc_final: 0.6982 (m) REVERT: A 576 VAL cc_start: 0.1563 (OUTLIER) cc_final: 0.1299 (p) REVERT: A 606 ASN cc_start: 0.7598 (t0) cc_final: 0.6847 (t0) REVERT: A 616 ASN cc_start: 0.5350 (m-40) cc_final: 0.5065 (m-40) REVERT: A 712 ILE cc_start: 0.7801 (pt) cc_final: 0.7582 (tp) REVERT: A 734 THR cc_start: 0.7452 (m) cc_final: 0.7180 (m) REVERT: A 821 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6658 (tt) REVERT: A 900 MET cc_start: 0.2202 (mmp) cc_final: 0.1994 (mmm) REVERT: A 1095 PHE cc_start: 0.5012 (t80) cc_final: 0.4564 (t80) REVERT: A 1109 PHE cc_start: 0.5939 (t80) cc_final: 0.5531 (t80) REVERT: D 41 ARG cc_start: 0.6794 (mtm110) cc_final: 0.6469 (mtm180) REVERT: D 69 PHE cc_start: 0.8031 (m-80) cc_final: 0.7824 (m-80) outliers start: 35 outliers final: 26 residues processed: 153 average time/residue: 0.1946 time to fit residues: 42.9528 Evaluate side-chains 149 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP 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 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 367 VAL Chi-restraints excluded: chain A residue 462 LYS 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 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU 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 888 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 115 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 928 ASN ** 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 = 0.5207 r_free = 0.5207 target = 0.303902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.268108 restraints weight = 19109.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.274405 restraints weight = 13420.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.275529 restraints weight = 9574.038| |-----------------------------------------------------------------------------| r_work (final): 0.4990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4625 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9262 Z= 0.155 Angle : 0.831 14.939 12602 Z= 0.432 Chirality : 0.049 0.247 1427 Planarity : 0.006 0.113 1636 Dihedral : 7.479 63.394 1254 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.64 % Favored : 84.84 % Rotamer: Outliers : 4.08 % Allowed : 20.20 % Favored : 75.72 % 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: -3.85 (0.22), residues: 1154 helix: -0.71 (0.33), residues: 207 sheet: -2.36 (0.35), residues: 198 loop : -3.38 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS A 655 PHE 0.023 0.002 PHE A 906 TYR 0.038 0.002 TYR A 91 ARG 0.008 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 237) hydrogen bonds : angle 6.56388 ( 672) SS BOND : bond 0.00591 ( 9) SS BOND : angle 1.61690 ( 18) covalent geometry : bond 0.00324 ( 9253) covalent geometry : angle 0.82959 (12584) *********************** 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 165 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1038 (OUTLIER) cc_final: 0.0035 (tttm) REVERT: A 275 PHE cc_start: 0.1199 (OUTLIER) cc_final: 0.0844 (m-80) REVERT: A 307 THR cc_start: 0.7223 (OUTLIER) cc_final: 0.6978 (m) REVERT: A 576 VAL cc_start: 0.1583 (OUTLIER) cc_final: 0.1295 (p) REVERT: A 606 ASN cc_start: 0.7706 (t0) cc_final: 0.7045 (t0) REVERT: A 616 ASN cc_start: 0.5405 (m-40) cc_final: 0.5115 (m-40) REVERT: A 643 PHE cc_start: 0.5839 (t80) cc_final: 0.5636 (t80) REVERT: A 712 ILE cc_start: 0.7780 (pt) cc_final: 0.7569 (tp) REVERT: A 734 THR cc_start: 0.7406 (m) cc_final: 0.7189 (m) REVERT: A 938 LEU cc_start: 0.5751 (mp) cc_final: 0.5268 (mp) REVERT: A 1095 PHE cc_start: 0.5114 (t80) cc_final: 0.4592 (t80) REVERT: D 4 GLN cc_start: 0.6795 (tp-100) cc_final: 0.6530 (tp-100) REVERT: D 41 ARG cc_start: 0.6834 (mtm110) cc_final: 0.6551 (mtm180) outliers start: 41 outliers final: 28 residues processed: 158 average time/residue: 0.1946 time to fit residues: 44.3737 Evaluate side-chains 150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 LYS 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 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 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 726 ILE 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 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 906 PHE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 22 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** 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 = 0.5189 r_free = 0.5189 target = 0.302040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.263474 restraints weight = 18537.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.269373 restraints weight = 12258.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.273506 restraints weight = 8907.117| |-----------------------------------------------------------------------------| r_work (final): 0.4978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4592 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9262 Z= 0.157 Angle : 0.856 19.102 12602 Z= 0.441 Chirality : 0.049 0.241 1427 Planarity : 0.006 0.114 1636 Dihedral : 7.455 63.563 1254 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.42 % Favored : 83.97 % Rotamer: Outliers : 3.68 % Allowed : 20.90 % Favored : 75.42 % 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: -3.75 (0.23), residues: 1154 helix: -0.65 (0.33), residues: 207 sheet: -2.30 (0.36), residues: 196 loop : -3.31 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 37 HIS 0.003 0.001 HIS A 655 PHE 0.021 0.002 PHE A 275 TYR 0.040 0.002 TYR A 91 ARG 0.009 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 237) hydrogen bonds : angle 6.55287 ( 672) SS BOND : bond 0.00553 ( 9) SS BOND : angle 1.51960 ( 18) covalent geometry : bond 0.00335 ( 9253) covalent geometry : angle 0.85440 (12584) *********************** 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 164 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1027 (OUTLIER) cc_final: -0.0043 (tttm) REVERT: A 275 PHE cc_start: 0.1782 (OUTLIER) cc_final: 0.1360 (m-80) REVERT: A 307 THR cc_start: 0.7192 (OUTLIER) cc_final: 0.6902 (m) REVERT: A 338 PHE cc_start: 0.5945 (t80) cc_final: 0.5698 (p90) REVERT: A 576 VAL cc_start: 0.1381 (OUTLIER) cc_final: 0.1107 (p) REVERT: A 606 ASN cc_start: 0.7564 (t0) cc_final: 0.6974 (t0) REVERT: A 616 ASN cc_start: 0.5525 (m-40) cc_final: 0.5235 (m-40) REVERT: A 643 PHE cc_start: 0.5854 (t80) cc_final: 0.5632 (t80) REVERT: A 707 TYR cc_start: 0.5087 (t80) cc_final: 0.4832 (m-10) REVERT: A 712 ILE cc_start: 0.7996 (pt) cc_final: 0.7720 (tp) REVERT: A 734 THR cc_start: 0.7739 (m) cc_final: 0.7479 (m) REVERT: A 938 LEU cc_start: 0.5778 (mp) cc_final: 0.5453 (mp) REVERT: A 1095 PHE cc_start: 0.5151 (t80) cc_final: 0.4614 (t80) outliers start: 37 outliers final: 30 residues processed: 158 average time/residue: 0.2215 time to fit residues: 51.3103 Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP 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 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 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 461 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 726 ILE 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 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 906 PHE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1018 ILE 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 34 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.306945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.271222 restraints weight = 18106.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.276363 restraints weight = 12271.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.280271 restraints weight = 9020.865| |-----------------------------------------------------------------------------| r_work (final): 0.4962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4607 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9262 Z= 0.168 Angle : 0.864 14.780 12602 Z= 0.448 Chirality : 0.050 0.238 1427 Planarity : 0.006 0.114 1636 Dihedral : 7.436 64.061 1254 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.25 % Favored : 84.14 % Rotamer: Outliers : 3.38 % Allowed : 21.49 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.90 % 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: -0.65 (0.33), residues: 207 sheet: -2.29 (0.35), residues: 203 loop : -3.34 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.004 0.001 HIS A 655 PHE 0.023 0.002 PHE A 906 TYR 0.037 0.002 TYR A 91 ARG 0.010 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04998 ( 237) hydrogen bonds : angle 6.57532 ( 672) SS BOND : bond 0.00557 ( 9) SS BOND : angle 1.48928 ( 18) covalent geometry : bond 0.00363 ( 9253) covalent geometry : angle 0.86310 (12584) ********************** 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 153 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.0915 (OUTLIER) cc_final: -0.0105 (tttm) REVERT: A 275 PHE cc_start: 0.2059 (OUTLIER) cc_final: 0.1537 (m-80) REVERT: A 307 THR cc_start: 0.7307 (OUTLIER) cc_final: 0.7049 (m) REVERT: A 338 PHE cc_start: 0.6017 (t80) cc_final: 0.5746 (p90) REVERT: A 606 ASN cc_start: 0.7451 (t0) cc_final: 0.6793 (t0) REVERT: A 616 ASN cc_start: 0.5157 (m-40) cc_final: 0.4843 (m-40) REVERT: A 643 PHE cc_start: 0.5895 (t80) cc_final: 0.5655 (t80) REVERT: A 707 TYR cc_start: 0.5119 (t80) cc_final: 0.4891 (m-10) REVERT: A 712 ILE cc_start: 0.7941 (pt) cc_final: 0.7635 (tp) REVERT: A 734 THR cc_start: 0.8043 (m) cc_final: 0.7762 (m) REVERT: A 1095 PHE cc_start: 0.5169 (t80) cc_final: 0.4661 (t80) REVERT: D 41 ARG cc_start: 0.6596 (mtm110) cc_final: 0.5497 (mtt180) outliers start: 34 outliers final: 30 residues processed: 147 average time/residue: 0.2253 time to fit residues: 48.5826 Evaluate side-chains 151 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 ASP 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 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 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 461 LEU Chi-restraints excluded: chain A residue 525 CYS 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 726 ILE 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 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 906 PHE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1018 ILE 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: 0.9980 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 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 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** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5214 r_free = 0.5214 target = 0.304619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.267825 restraints weight = 17996.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.273091 restraints weight = 12263.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.4987 r_free = 0.4987 target = 0.277125 restraints weight = 9121.813| |-----------------------------------------------------------------------------| r_work (final): 0.5002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4590 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9262 Z= 0.160 Angle : 0.845 15.859 12602 Z= 0.438 Chirality : 0.049 0.233 1427 Planarity : 0.006 0.114 1636 Dihedral : 7.347 63.988 1254 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.73 % Favored : 84.66 % Rotamer: Outliers : 3.28 % Allowed : 21.39 % Favored : 75.32 % 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: -3.75 (0.23), residues: 1154 helix: -0.64 (0.34), residues: 207 sheet: -2.22 (0.36), residues: 202 loop : -3.34 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS A 655 PHE 0.022 0.002 PHE A 906 TYR 0.034 0.002 TYR A 91 ARG 0.014 0.001 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.04836 ( 237) hydrogen bonds : angle 6.44575 ( 672) SS BOND : bond 0.00513 ( 9) SS BOND : angle 1.40924 ( 18) covalent geometry : bond 0.00342 ( 9253) covalent geometry : angle 0.84415 (12584) =============================================================================== Job complete usr+sys time: 3972.18 seconds wall clock time: 70 minutes 50.14 seconds (4250.14 seconds total)