Starting phenix.real_space_refine on Wed Sep 17 14:48:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fg3_31577/09_2025/7fg3_31577.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fg3_31577/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7fg3_31577/09_2025/7fg3_31577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fg3_31577/09_2025/7fg3_31577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fg3_31577/09_2025/7fg3_31577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fg3_31577/09_2025/7fg3_31577.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.84, per 1000 atoms: 0.20 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: 0.89 Conformation dependent library (CDL) restraints added in 360.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 1.65 Time building geometry restraints manager: 1.15 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: 1.200 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.210 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.810 ------------------------------------------------------------------------------- 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 : 37.18 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG A 634 TYR 0.069 0.003 TYR A 449 PHE 0.053 0.003 PHE A 898 TRP 0.022 0.003 TRP A 353 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 9253) covalent geometry : angle 1.13302 (12584) SS BOND : bond 0.06015 ( 9) SS BOND : angle 2.97875 ( 18) hydrogen bonds : bond 0.24804 ( 237) hydrogen bonds : angle 11.23295 ( 672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.258 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: 0.0555 (mmt) REVERT: A 200 TYR cc_start: 0.3442 (t80) cc_final: 0.2550 (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: 0.7273 (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: 0.5422 (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: 0.0762 time to fit residues: 16.9550 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 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 = 0.5211 r_free = 0.5211 target = 0.303756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.266632 restraints weight = 18145.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.272295 restraints weight = 12103.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4989 r_free = 0.4989 target = 0.276053 restraints weight = 9040.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.278588 restraints weight = 7245.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5019 r_free = 0.5019 target = 0.279859 restraints weight = 6172.711| |-----------------------------------------------------------------------------| r_work (final): 0.5070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4498 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9262 Z= 0.195 Angle : 0.908 14.997 12602 Z= 0.487 Chirality : 0.052 0.263 1427 Planarity : 0.007 0.107 1636 Dihedral : 8.624 66.051 1254 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.78 % Allowed : 15.51 % Favored : 83.71 % Rotamer: Outliers : 1.49 % Allowed : 11.74 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 1.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.17 (0.22), residues: 1154 helix: -1.29 (0.33), residues: 199 sheet: -2.48 (0.36), residues: 167 loop : -3.50 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 237 TYR 0.028 0.002 TYR A 204 PHE 0.042 0.002 PHE A 823 TRP 0.015 0.002 TRP A 353 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9253) covalent geometry : angle 0.90525 (12584) SS BOND : bond 0.00676 ( 9) SS BOND : angle 1.95077 ( 18) hydrogen bonds : bond 0.06305 ( 237) hydrogen bonds : angle 8.06229 ( 672) *********************** 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 159 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.1758 (mmt) cc_final: 0.1021 (mmt) REVERT: A 200 TYR cc_start: 0.3569 (t80) cc_final: 0.2068 (m-80) REVERT: A 224 GLU cc_start: 0.5815 (pm20) cc_final: 0.5606 (pm20) REVERT: A 307 THR cc_start: 0.7089 (m) cc_final: 0.6775 (m) REVERT: A 313 TYR cc_start: 0.6188 (m-10) cc_final: 0.5941 (m-10) REVERT: A 598 ILE cc_start: 0.5368 (mt) cc_final: 0.4658 (mp) REVERT: A 656 VAL cc_start: 0.7323 (p) cc_final: 0.6749 (t) REVERT: A 1017 GLU cc_start: 0.6105 (pp20) cc_final: 0.5900 (pp20) REVERT: A 1019 ARG cc_start: 0.6937 (ttp-110) cc_final: 0.6674 (ttp-110) REVERT: A 1109 PHE cc_start: 0.5105 (t80) cc_final: 0.4899 (t80) outliers start: 15 outliers final: 7 residues processed: 150 average time/residue: 0.0968 time to fit residues: 20.3595 Evaluate side-chains 128 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain D residue 6 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 111 optimal weight: 9.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 955 ASN A1036 GLN A1048 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 = 0.5208 r_free = 0.5208 target = 0.303626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.265744 restraints weight = 18125.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.271516 restraints weight = 12191.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.275718 restraints weight = 9038.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.278371 restraints weight = 7142.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.279736 restraints weight = 6028.183| |-----------------------------------------------------------------------------| r_work (final): 0.5035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4507 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9262 Z= 0.172 Angle : 0.849 14.864 12602 Z= 0.452 Chirality : 0.049 0.265 1427 Planarity : 0.006 0.112 1636 Dihedral : 8.127 64.849 1254 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.42 % Favored : 83.88 % Rotamer: Outliers : 2.69 % Allowed : 15.52 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.81 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.98 (0.22), residues: 1154 helix: -1.04 (0.33), residues: 204 sheet: -2.35 (0.37), residues: 180 loop : -3.42 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 815 TYR 0.021 0.002 TYR A 449 PHE 0.026 0.002 PHE A 541 TRP 0.013 0.001 TRP A 353 HIS 0.006 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9253) covalent geometry : angle 0.84749 (12584) SS BOND : bond 0.00444 ( 9) SS BOND : angle 1.56965 ( 18) hydrogen bonds : bond 0.05699 ( 237) hydrogen bonds : angle 7.37497 ( 672) *********************** 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 154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.3702 (t80) cc_final: 0.1987 (m-80) REVERT: A 226 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7456 (mp) REVERT: A 307 THR cc_start: 0.6939 (m) cc_final: 0.6649 (m) REVERT: A 406 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6382 (tm-30) REVERT: A 1109 PHE cc_start: 0.5200 (t80) cc_final: 0.4968 (t80) REVERT: D 41 ARG cc_start: 0.6869 (mtm110) cc_final: 0.6489 (mtm180) outliers start: 27 outliers final: 14 residues processed: 148 average time/residue: 0.0860 time to fit residues: 18.3003 Evaluate side-chains 128 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1054 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5194 r_free = 0.5194 target = 0.301922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.262124 restraints weight = 18119.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.268606 restraints weight = 11673.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.273091 restraints weight = 8345.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.276039 restraints weight = 6489.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.277695 restraints weight = 5403.527| |-----------------------------------------------------------------------------| r_work (final): 0.5052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4518 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9262 Z= 0.171 Angle : 0.852 14.704 12602 Z= 0.446 Chirality : 0.050 0.265 1427 Planarity : 0.006 0.111 1636 Dihedral : 7.892 65.110 1254 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.34 % Favored : 83.97 % Rotamer: Outliers : 4.38 % Allowed : 15.42 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.22), residues: 1154 helix: -0.85 (0.33), residues: 206 sheet: -2.29 (0.37), residues: 180 loop : -3.45 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 765 TYR 0.021 0.002 TYR A 449 PHE 0.044 0.002 PHE A 275 TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9253) covalent geometry : angle 0.84826 (12584) SS BOND : bond 0.00717 ( 9) SS BOND : angle 2.16869 ( 18) hydrogen bonds : bond 0.05369 ( 237) hydrogen bonds : angle 7.03593 ( 672) *********************** 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 166 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.6807 (m) cc_final: 0.6561 (m) REVERT: A 321 GLN cc_start: 0.4198 (OUTLIER) cc_final: 0.3758 (tp-100) REVERT: A 402 ILE cc_start: 0.5947 (OUTLIER) cc_final: 0.5275 (tt) REVERT: A 576 VAL cc_start: 0.1721 (OUTLIER) cc_final: 0.1480 (p) REVERT: A 616 ASN cc_start: 0.4408 (m-40) cc_final: 0.4202 (m-40) REVERT: A 656 VAL cc_start: 0.7446 (p) cc_final: 0.6689 (t) REVERT: A 819 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6475 (mm-30) REVERT: A 916 LEU cc_start: -0.2870 (OUTLIER) cc_final: -0.3163 (tt) REVERT: A 954 GLN cc_start: 0.7540 (mt0) cc_final: 0.7328 (mt0) REVERT: A 1095 PHE cc_start: 0.5737 (t80) cc_final: 0.5208 (t80) REVERT: A 1109 PHE cc_start: 0.5301 (t80) cc_final: 0.5000 (t80) REVERT: D 41 ARG cc_start: 0.6637 (mtm110) cc_final: 0.6213 (mtm180) outliers start: 44 outliers final: 21 residues processed: 157 average time/residue: 0.0840 time to fit residues: 19.3164 Evaluate side-chains 143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 458 LYS 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 597 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 6 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 110 optimal weight: 0.0470 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 928 ASN A1054 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.302591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.265082 restraints weight = 18507.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.271201 restraints weight = 12091.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.275156 restraints weight = 8764.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.5002 r_free = 0.5002 target = 0.278027 restraints weight = 6903.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.280054 restraints weight = 5754.598| |-----------------------------------------------------------------------------| r_work (final): 0.5060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4467 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9262 Z= 0.160 Angle : 0.839 14.584 12602 Z= 0.438 Chirality : 0.049 0.259 1427 Planarity : 0.006 0.111 1636 Dihedral : 7.618 64.189 1254 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.60 % Favored : 83.88 % Rotamer: Outliers : 5.07 % Allowed : 15.82 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.23), residues: 1154 helix: -0.74 (0.34), residues: 205 sheet: -2.30 (0.35), residues: 195 loop : -3.38 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 765 TYR 0.037 0.002 TYR A 91 PHE 0.033 0.002 PHE A 275 TRP 0.008 0.001 TRP D 107 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9253) covalent geometry : angle 0.83467 (12584) SS BOND : bond 0.00733 ( 9) SS BOND : angle 2.45124 ( 18) hydrogen bonds : bond 0.05110 ( 237) hydrogen bonds : angle 6.72084 ( 672) *********************** 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 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.326 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: 0.0997 (OUTLIER) cc_final: 0.0009 (tttm) REVERT: A 307 THR cc_start: 0.6853 (m) cc_final: 0.6567 (m) REVERT: A 402 ILE cc_start: 0.6224 (OUTLIER) cc_final: 0.5888 (tt) REVERT: A 406 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7194 (tm-30) REVERT: A 576 VAL cc_start: 0.1347 (OUTLIER) cc_final: 0.1083 (p) REVERT: A 606 ASN cc_start: 0.6972 (t0) cc_final: 0.6403 (t0) REVERT: A 656 VAL cc_start: 0.7247 (p) cc_final: 0.6573 (t) REVERT: A 699 LEU cc_start: 0.4398 (OUTLIER) cc_final: 0.4075 (pp) REVERT: A 712 ILE cc_start: 0.7840 (pt) cc_final: 0.7611 (tp) REVERT: A 819 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.6074 (mm-30) REVERT: A 1095 PHE cc_start: 0.6013 (t80) cc_final: 0.5748 (t80) REVERT: A 1109 PHE cc_start: 0.5252 (t80) cc_final: 0.4928 (t80) REVERT: D 41 ARG cc_start: 0.6668 (mtm110) cc_final: 0.6280 (mtm180) outliers start: 51 outliers final: 25 residues processed: 174 average time/residue: 0.0885 time to fit residues: 22.3052 Evaluate side-chains 150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU 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 615 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 928 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 762 GLN A 928 ASN A1054 GLN ** 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 = 0.5217 r_free = 0.5217 target = 0.304361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.268310 restraints weight = 19376.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.273765 restraints weight = 13014.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.277540 restraints weight = 9542.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.279840 restraints weight = 7588.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.281615 restraints weight = 6442.563| |-----------------------------------------------------------------------------| r_work (final): 0.5006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4566 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9262 Z= 0.181 Angle : 0.881 17.978 12602 Z= 0.455 Chirality : 0.050 0.263 1427 Planarity : 0.006 0.109 1636 Dihedral : 7.715 63.354 1254 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.12 % Favored : 83.36 % Rotamer: Outliers : 3.98 % Allowed : 18.01 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.81 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.22), residues: 1154 helix: -0.89 (0.32), residues: 207 sheet: -2.37 (0.34), residues: 202 loop : -3.40 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 765 TYR 0.016 0.002 TYR A 449 PHE 0.025 0.002 PHE A 275 TRP 0.010 0.001 TRP A 353 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9253) covalent geometry : angle 0.87814 (12584) SS BOND : bond 0.00650 ( 9) SS BOND : angle 2.05356 ( 18) hydrogen bonds : bond 0.05340 ( 237) hydrogen bonds : angle 6.75596 ( 672) *********************** 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 161 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.364 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 182 LYS cc_start: 0.1076 (OUTLIER) cc_final: 0.0108 (tttm) REVERT: A 204 TYR cc_start: 0.5877 (m-80) cc_final: 0.5177 (m-80) REVERT: A 307 THR cc_start: 0.6961 (m) cc_final: 0.6706 (m) REVERT: A 576 VAL cc_start: 0.1216 (OUTLIER) cc_final: 0.0940 (p) REVERT: A 606 ASN cc_start: 0.7189 (t0) cc_final: 0.6528 (t0) REVERT: A 656 VAL cc_start: 0.7500 (p) cc_final: 0.6916 (t) REVERT: A 699 LEU cc_start: 0.4695 (OUTLIER) cc_final: 0.4461 (pp) REVERT: A 712 ILE cc_start: 0.8056 (pt) cc_final: 0.7745 (tp) REVERT: A 734 THR cc_start: 0.7683 (m) cc_final: 0.7336 (m) REVERT: A 1109 PHE cc_start: 0.5568 (t80) cc_final: 0.5245 (t80) REVERT: D 41 ARG cc_start: 0.6645 (mtm110) cc_final: 0.6283 (mtm180) outliers start: 40 outliers final: 25 residues processed: 153 average time/residue: 0.0900 time to fit residues: 19.7601 Evaluate side-chains 147 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 927 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 5 LEU 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 22 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** A1010 GLN ** 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 = 0.5208 r_free = 0.5208 target = 0.303322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.268046 restraints weight = 19004.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.273000 restraints weight = 13353.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.274125 restraints weight = 9372.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.275804 restraints weight = 7944.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.275856 restraints weight = 8242.440| |-----------------------------------------------------------------------------| r_work (final): 0.4976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4640 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9262 Z= 0.172 Angle : 0.856 14.842 12602 Z= 0.445 Chirality : 0.050 0.255 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.559 62.914 1254 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.60 % Favored : 83.80 % Rotamer: Outliers : 3.78 % Allowed : 19.40 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.22), residues: 1154 helix: -0.84 (0.33), residues: 206 sheet: -2.36 (0.35), residues: 197 loop : -3.34 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 765 TYR 0.018 0.002 TYR A 741 PHE 0.022 0.002 PHE A 338 TRP 0.008 0.001 TRP A 353 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9253) covalent geometry : angle 0.85396 (12584) SS BOND : bond 0.00624 ( 9) SS BOND : angle 1.80390 ( 18) hydrogen bonds : bond 0.05141 ( 237) hydrogen bonds : angle 6.65788 ( 672) *********************** 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 162 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.332 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 182 LYS cc_start: 0.1062 (OUTLIER) cc_final: 0.0082 (tttm) REVERT: A 204 TYR cc_start: 0.5965 (m-80) cc_final: 0.5274 (m-80) REVERT: A 307 THR cc_start: 0.7174 (m) cc_final: 0.6959 (m) REVERT: A 576 VAL cc_start: 0.1095 (OUTLIER) cc_final: 0.0771 (p) REVERT: A 606 ASN cc_start: 0.7464 (t0) cc_final: 0.6493 (t0) REVERT: A 643 PHE cc_start: 0.5852 (t80) cc_final: 0.5642 (t80) REVERT: A 656 VAL cc_start: 0.7404 (p) cc_final: 0.6842 (t) REVERT: A 699 LEU cc_start: 0.5124 (OUTLIER) cc_final: 0.4883 (pp) REVERT: A 712 ILE cc_start: 0.7835 (pt) cc_final: 0.7613 (tp) REVERT: A 734 THR cc_start: 0.7598 (m) cc_final: 0.7368 (m) REVERT: A 900 MET cc_start: 0.1583 (mmp) cc_final: 0.1338 (mmm) REVERT: A 1095 PHE cc_start: 0.4659 (t80) cc_final: 0.4444 (t80) REVERT: A 1109 PHE cc_start: 0.5541 (t80) cc_final: 0.5135 (t80) REVERT: D 41 ARG cc_start: 0.6699 (mtm110) cc_final: 0.6342 (mtm180) REVERT: D 71 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8869 (tp) outliers start: 38 outliers final: 28 residues processed: 153 average time/residue: 0.0839 time to fit residues: 18.8056 Evaluate side-chains 146 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 289 VAL 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 409 GLN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 461 LEU 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 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 699 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 906 PHE Chi-restraints excluded: chain A residue 928 ASN 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 Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 71 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 0.0040 chunk 108 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN A1083 HIS D 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5215 r_free = 0.5215 target = 0.304312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.268051 restraints weight = 18900.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.273376 restraints weight = 13267.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.278079 restraints weight = 8594.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.277591 restraints weight = 7354.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.277753 restraints weight = 7082.023| |-----------------------------------------------------------------------------| r_work (final): 0.4974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4642 moved from start: 0.4651 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= 0.168 Angle : 0.864 17.207 12602 Z= 0.447 Chirality : 0.049 0.264 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.559 62.999 1254 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.51 % Favored : 83.88 % Rotamer: Outliers : 4.28 % Allowed : 19.90 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.81 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.23), residues: 1154 helix: -0.71 (0.33), residues: 208 sheet: -2.35 (0.35), residues: 197 loop : -3.30 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 765 TYR 0.018 0.002 TYR A 873 PHE 0.023 0.002 PHE A 275 TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9253) covalent geometry : angle 0.86206 (12584) SS BOND : bond 0.00574 ( 9) SS BOND : angle 1.66906 ( 18) hydrogen bonds : bond 0.05061 ( 237) hydrogen bonds : angle 6.56258 ( 672) *********************** 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: 43 poor density : 122 time to evaluate : 0.332 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: 0.1171 (OUTLIER) cc_final: 0.0114 (tttm) REVERT: A 275 PHE cc_start: 0.0867 (OUTLIER) cc_final: 0.0569 (m-80) REVERT: A 307 THR cc_start: 0.7207 (m) cc_final: 0.6978 (m) REVERT: A 321 GLN cc_start: 0.4231 (OUTLIER) cc_final: 0.3989 (tp40) REVERT: A 606 ASN cc_start: 0.7729 (t0) cc_final: 0.6846 (t0) REVERT: A 643 PHE cc_start: 0.5912 (t80) cc_final: 0.5684 (t80) REVERT: A 656 VAL cc_start: 0.7442 (p) cc_final: 0.6923 (t) REVERT: A 712 ILE cc_start: 0.7924 (pt) cc_final: 0.7684 (tp) REVERT: A 734 THR cc_start: 0.7583 (m) cc_final: 0.7282 (m) REVERT: A 900 MET cc_start: 0.2015 (mmp) cc_final: 0.1761 (mmm) REVERT: A 938 LEU cc_start: 0.5486 (mp) cc_final: 0.5187 (mp) REVERT: A 1095 PHE cc_start: 0.5177 (t80) cc_final: 0.4806 (t80) REVERT: D 4 GLN cc_start: 0.6843 (tp-100) cc_final: 0.6574 (tp-100) REVERT: D 31 SER cc_start: 0.6257 (OUTLIER) cc_final: 0.5285 (t) REVERT: D 41 ARG cc_start: 0.6713 (mtm110) cc_final: 0.6449 (mtm180) outliers start: 43 outliers final: 30 residues processed: 157 average time/residue: 0.0827 time to fit residues: 18.8990 Evaluate side-chains 150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL 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 321 GLN Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 THR 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 1018 ILE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 100 optimal weight: 0.7980 chunk 110 optimal weight: 0.0050 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.2782 ------------------------------------------------------------------------------- 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 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 = 0.5205 r_free = 0.5205 target = 0.304380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.266929 restraints weight = 18482.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.272870 restraints weight = 12180.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.277100 restraints weight = 8818.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.280017 restraints weight = 6866.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.282014 restraints weight = 5702.328| |-----------------------------------------------------------------------------| r_work (final): 0.5040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4413 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9262 Z= 0.157 Angle : 0.867 15.073 12602 Z= 0.446 Chirality : 0.049 0.254 1427 Planarity : 0.006 0.109 1636 Dihedral : 7.384 62.749 1254 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.86 % Favored : 85.62 % Rotamer: Outliers : 3.18 % Allowed : 21.59 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.23), residues: 1154 helix: -0.33 (0.34), residues: 206 sheet: -2.33 (0.35), residues: 196 loop : -3.24 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 765 TYR 0.025 0.002 TYR A 91 PHE 0.025 0.001 PHE A 927 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9253) covalent geometry : angle 0.86573 (12584) SS BOND : bond 0.00552 ( 9) SS BOND : angle 1.45062 ( 18) hydrogen bonds : bond 0.04714 ( 237) hydrogen bonds : angle 6.38047 ( 672) *********************** 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 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.4145 (m-10) cc_final: 0.3881 (m-10) REVERT: A 182 LYS cc_start: 0.1202 (OUTLIER) cc_final: 0.0011 (tttm) REVERT: A 204 TYR cc_start: 0.5907 (m-80) cc_final: 0.4680 (m-80) REVERT: A 275 PHE cc_start: 0.1038 (OUTLIER) cc_final: 0.0605 (m-80) REVERT: A 307 THR cc_start: 0.7198 (m) cc_final: 0.6905 (m) REVERT: A 602 THR cc_start: 0.6998 (OUTLIER) cc_final: 0.6751 (p) REVERT: A 606 ASN cc_start: 0.7344 (t0) cc_final: 0.6717 (t0) REVERT: A 712 ILE cc_start: 0.7963 (pt) cc_final: 0.7730 (tp) REVERT: A 731 MET cc_start: 0.7737 (mmp) cc_final: 0.7289 (mmp) REVERT: A 734 THR cc_start: 0.7462 (m) cc_final: 0.7223 (m) REVERT: A 900 MET cc_start: 0.2348 (mmp) cc_final: 0.2028 (mmm) REVERT: A 938 LEU cc_start: 0.5042 (mp) cc_final: 0.4442 (mp) REVERT: A 1095 PHE cc_start: 0.5191 (t80) cc_final: 0.4871 (t80) REVERT: D 4 GLN cc_start: 0.6776 (tp-100) cc_final: 0.6574 (tp-100) outliers start: 32 outliers final: 24 residues processed: 156 average time/residue: 0.0887 time to fit residues: 19.9972 Evaluate side-chains 143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL 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 276 LEU Chi-restraints excluded: chain A residue 289 VAL 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 402 ILE Chi-restraints excluded: chain A residue 469 SER 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 585 LEU Chi-restraints excluded: chain A residue 602 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 8.9990 chunk 33 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.0970 chunk 80 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1054 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5216 r_free = 0.5216 target = 0.305360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.268261 restraints weight = 18684.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.274049 restraints weight = 12466.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.278129 restraints weight = 9011.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.280972 restraints weight = 7015.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.282655 restraints weight = 5836.588| |-----------------------------------------------------------------------------| r_work (final): 0.5082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4404 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9262 Z= 0.152 Angle : 0.872 15.110 12602 Z= 0.445 Chirality : 0.049 0.252 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.289 62.982 1254 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.56 % Favored : 84.92 % Rotamer: Outliers : 2.99 % Allowed : 22.39 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.81 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.23), residues: 1154 helix: -0.19 (0.34), residues: 207 sheet: -2.25 (0.35), residues: 196 loop : -3.22 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 765 TYR 0.028 0.002 TYR A 91 PHE 0.056 0.002 PHE A 55 TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9253) covalent geometry : angle 0.87096 (12584) SS BOND : bond 0.00495 ( 9) SS BOND : angle 1.36969 ( 18) hydrogen bonds : bond 0.04730 ( 237) hydrogen bonds : angle 6.36597 ( 672) ********************** 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 147 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.4062 (m-10) cc_final: 0.3792 (m-10) REVERT: A 182 LYS cc_start: 0.1106 (OUTLIER) cc_final: -0.0124 (tttm) REVERT: A 307 THR cc_start: 0.7060 (m) cc_final: 0.6732 (m) REVERT: A 602 THR cc_start: 0.6923 (OUTLIER) cc_final: 0.6716 (p) REVERT: A 606 ASN cc_start: 0.7337 (t0) cc_final: 0.6700 (t0) REVERT: A 712 ILE cc_start: 0.7865 (pt) cc_final: 0.7640 (tp) REVERT: A 731 MET cc_start: 0.7506 (mmp) cc_final: 0.6976 (mmp) REVERT: A 854 LYS cc_start: 0.5648 (pttp) cc_final: 0.5416 (pttp) REVERT: A 900 MET cc_start: 0.2510 (mmp) cc_final: 0.2284 (mmm) REVERT: A 938 LEU cc_start: 0.5018 (mp) cc_final: 0.4425 (mp) REVERT: A 1095 PHE cc_start: 0.5173 (t80) cc_final: 0.4899 (t80) REVERT: D 41 ARG cc_start: 0.6904 (mtm110) cc_final: 0.6576 (mtm180) outliers start: 30 outliers final: 26 residues processed: 143 average time/residue: 0.0941 time to fit residues: 19.1257 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL 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 276 LEU Chi-restraints excluded: chain A residue 289 VAL 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 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 585 LEU Chi-restraints excluded: chain A residue 602 THR 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 906 PHE Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 30 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5207 r_free = 0.5207 target = 0.304297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.271387 restraints weight = 18464.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.275044 restraints weight = 12313.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.276473 restraints weight = 9126.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.276719 restraints weight = 7632.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.277294 restraints weight = 7640.411| |-----------------------------------------------------------------------------| r_work (final): 0.5057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9262 Z= 0.160 Angle : 0.868 15.084 12602 Z= 0.448 Chirality : 0.050 0.249 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.270 63.211 1254 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.95 % Favored : 85.44 % Rotamer: Outliers : 2.79 % Allowed : 23.28 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.23), residues: 1154 helix: -0.18 (0.34), residues: 208 sheet: -2.16 (0.36), residues: 192 loop : -3.22 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 765 TYR 0.025 0.002 TYR A 91 PHE 0.044 0.002 PHE A 55 TRP 0.006 0.001 TRP A 353 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 9253) covalent geometry : angle 0.86737 (12584) SS BOND : bond 0.00520 ( 9) SS BOND : angle 1.42631 ( 18) hydrogen bonds : bond 0.04600 ( 237) hydrogen bonds : angle 6.32479 ( 672) =============================================================================== Job complete usr+sys time: 2266.84 seconds wall clock time: 39 minutes 42.99 seconds (2382.99 seconds total)