Starting phenix.real_space_refine on Wed Sep 25 01:12:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/09_2024/7fg3_31577.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/09_2024/7fg3_31577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/09_2024/7fg3_31577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/09_2024/7fg3_31577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/09_2024/7fg3_31577.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/09_2024/7fg3_31577.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 5750 2.51 5 N 1523 2.21 5 O 1741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9054 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8180 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 49, 'TRANS': 1000} Chain breaks: 4 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 874 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Time building chain proxies: 5.52, per 1000 atoms: 0.61 Number of scatterers: 9054 At special positions: 0 Unit cell: (116.604, 110.916, 160.686, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1741 8.00 N 1523 7.00 C 5750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.21 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 985.5 milliseconds 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: 0.99 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: 2.97 Time building geometry restraints manager: 2.53 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: 1.150 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.770 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 9253 Z= 0.358 Angle : 1.133 20.164 12584 Z= 0.664 Chirality : 0.057 0.364 1427 Planarity : 0.008 0.137 1636 Dihedral : 14.472 86.613 3300 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 37.29 Ramachandran Plot: Outliers : 0.69 % Allowed : 18.54 % Favored : 80.76 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 1.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.21), residues: 1154 helix: -1.71 (0.32), residues: 196 sheet: -2.70 (0.33), residues: 179 loop : -3.79 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 353 HIS 0.006 0.001 HIS A 655 PHE 0.053 0.003 PHE A 898 TYR 0.069 0.003 TYR A 449 ARG 0.011 0.001 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0764 (mmt) cc_final: 0.0560 (mmt) REVERT: A 200 TYR cc_start: 0.3442 (t80) cc_final: 0.2549 (m-80) REVERT: A 204 TYR cc_start: 0.6108 (m-10) cc_final: 0.5800 (m-10) REVERT: A 307 THR cc_start: 0.7545 (m) cc_final: 0.7272 (m) REVERT: A 598 ILE cc_start: 0.3864 (mt) cc_final: 0.3372 (mp) REVERT: A 656 VAL cc_start: 0.7949 (p) cc_final: 0.7404 (t) REVERT: A 951 VAL cc_start: 0.5614 (t) cc_final: 0.5165 (t) REVERT: A 1109 PHE cc_start: 0.5974 (t80) cc_final: 0.5421 (t80) REVERT: D 5 LEU cc_start: 0.6436 (mp) cc_final: 0.6090 (mp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1996 time to fit residues: 43.6110 Evaluate side-chains 129 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 710 ASN A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4746 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9253 Z= 0.267 Angle : 0.913 15.086 12584 Z= 0.491 Chirality : 0.052 0.258 1427 Planarity : 0.007 0.107 1636 Dihedral : 8.666 65.982 1254 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.69 % Allowed : 16.38 % Favored : 82.93 % Rotamer: Outliers : 1.39 % Allowed : 11.54 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 1.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.22), residues: 1154 helix: -1.27 (0.33), residues: 200 sheet: -2.54 (0.36), residues: 166 loop : -3.51 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.007 0.001 HIS A1088 PHE 0.034 0.002 PHE A 823 TYR 0.027 0.002 TYR A 204 ARG 0.005 0.001 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 144 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0921 (mmt) cc_final: 0.0369 (mmt) REVERT: A 200 TYR cc_start: 0.3561 (t80) cc_final: 0.2013 (m-80) REVERT: A 307 THR cc_start: 0.7341 (m) cc_final: 0.7084 (m) REVERT: A 313 TYR cc_start: 0.5992 (m-10) cc_final: 0.5787 (m-10) REVERT: A 656 VAL cc_start: 0.7525 (p) cc_final: 0.7028 (t) REVERT: A 765 ARG cc_start: 0.6633 (mtt90) cc_final: 0.6302 (mtt90) REVERT: A 802 PHE cc_start: 0.6032 (m-80) cc_final: 0.5666 (m-80) REVERT: A 1019 ARG cc_start: 0.7053 (ttp-110) cc_final: 0.6795 (ttp-110) REVERT: A 1109 PHE cc_start: 0.5708 (t80) cc_final: 0.5229 (t80) outliers start: 14 outliers final: 8 residues processed: 148 average time/residue: 0.1902 time to fit residues: 40.1809 Evaluate side-chains 129 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 1088 HIS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A 955 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4715 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9253 Z= 0.233 Angle : 0.854 14.869 12584 Z= 0.453 Chirality : 0.050 0.297 1427 Planarity : 0.006 0.111 1636 Dihedral : 8.085 65.511 1254 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.16 % Favored : 84.14 % Rotamer: Outliers : 3.38 % Allowed : 14.23 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.22), residues: 1154 helix: -1.10 (0.32), residues: 204 sheet: -2.43 (0.37), residues: 175 loop : -3.39 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.007 0.001 HIS A1088 PHE 0.025 0.002 PHE A 541 TYR 0.020 0.002 TYR A 873 ARG 0.005 0.001 ARG A 815 *********************** 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 164 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 307 THR cc_start: 0.7097 (m) cc_final: 0.6855 (m) REVERT: A 406 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6708 (tm-30) REVERT: A 616 ASN cc_start: 0.4968 (m-40) cc_final: 0.4766 (m-40) REVERT: A 1109 PHE cc_start: 0.5757 (t80) cc_final: 0.5226 (t80) REVERT: D 41 ARG cc_start: 0.6554 (mtm110) cc_final: 0.6000 (mtm180) outliers start: 34 outliers final: 20 residues processed: 157 average time/residue: 0.1872 time to fit residues: 42.0138 Evaluate side-chains 139 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 469 SER 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 870 ILE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 50 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 0.0020 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 762 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1036 GLN A1048 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4711 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9253 Z= 0.227 Angle : 0.835 14.733 12584 Z= 0.439 Chirality : 0.049 0.259 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.837 65.475 1254 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.51 % Favored : 83.80 % Rotamer: Outliers : 4.28 % Allowed : 15.42 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.22), residues: 1154 helix: -0.74 (0.33), residues: 207 sheet: -2.27 (0.36), residues: 184 loop : -3.43 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1102 HIS 0.004 0.001 HIS A 207 PHE 0.033 0.002 PHE A 275 TYR 0.019 0.001 TYR A 873 ARG 0.003 0.000 ARG D 46 *********************** 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 172 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 129 time to evaluate : 0.912 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: 0.6966 (m) cc_final: 0.6759 (m) REVERT: A 576 VAL cc_start: 0.1403 (OUTLIER) cc_final: 0.1169 (p) REVERT: A 656 VAL cc_start: 0.7450 (p) cc_final: 0.6799 (t) REVERT: A 712 ILE cc_start: 0.8063 (pt) cc_final: 0.7765 (tp) REVERT: A 1095 PHE cc_start: 0.5314 (t80) cc_final: 0.5046 (t80) REVERT: A 1109 PHE cc_start: 0.5686 (t80) cc_final: 0.5191 (t80) REVERT: D 41 ARG cc_start: 0.6553 (mtm110) cc_final: 0.6060 (mtm180) outliers start: 43 outliers final: 19 residues processed: 165 average time/residue: 0.1888 time to fit residues: 44.8511 Evaluate side-chains 147 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.0270 chunk 1 optimal weight: 0.2980 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4783 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9253 Z= 0.247 Angle : 0.857 14.475 12584 Z= 0.450 Chirality : 0.050 0.253 1427 Planarity : 0.006 0.110 1636 Dihedral : 7.733 64.675 1254 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.12 % Favored : 83.36 % Rotamer: Outliers : 5.27 % Allowed : 16.02 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.23), residues: 1154 helix: -0.73 (0.33), residues: 205 sheet: -2.30 (0.35), residues: 196 loop : -3.38 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 107 HIS 0.004 0.001 HIS A 655 PHE 0.028 0.002 PHE A 275 TYR 0.018 0.002 TYR A 449 ARG 0.007 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 129 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.0957 (OUTLIER) cc_final: 0.0155 (tttm) REVERT: A 307 THR cc_start: 0.7277 (m) cc_final: 0.7071 (m) REVERT: A 606 ASN cc_start: 0.7601 (t0) cc_final: 0.7129 (t0) REVERT: A 656 VAL cc_start: 0.7697 (p) cc_final: 0.7188 (t) REVERT: A 699 LEU cc_start: 0.3857 (OUTLIER) cc_final: 0.3597 (pp) REVERT: A 712 ILE cc_start: 0.8132 (pt) cc_final: 0.7812 (tp) REVERT: A 773 GLU cc_start: 0.6600 (tt0) cc_final: 0.6305 (tt0) REVERT: A 1095 PHE cc_start: 0.5938 (t80) cc_final: 0.5568 (t80) REVERT: A 1109 PHE cc_start: 0.5996 (t80) cc_final: 0.5400 (t80) REVERT: D 41 ARG cc_start: 0.6568 (mtm110) cc_final: 0.6094 (mtm180) outliers start: 53 outliers final: 26 residues processed: 173 average time/residue: 0.1875 time to fit residues: 46.6777 Evaluate side-chains 148 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 449 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1011 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4789 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9253 Z= 0.240 Angle : 0.859 14.290 12584 Z= 0.449 Chirality : 0.051 0.330 1427 Planarity : 0.006 0.107 1636 Dihedral : 7.675 63.689 1254 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.25 % Favored : 84.23 % Rotamer: Outliers : 3.88 % Allowed : 17.71 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.81 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.23), residues: 1154 helix: -0.82 (0.32), residues: 208 sheet: -2.31 (0.35), residues: 200 loop : -3.34 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.004 0.001 HIS A 655 PHE 0.026 0.002 PHE A 275 TYR 0.040 0.002 TYR A 91 ARG 0.011 0.001 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.0854 (OUTLIER) cc_final: 0.0091 (tttm) REVERT: A 307 THR cc_start: 0.7290 (m) cc_final: 0.7088 (m) REVERT: A 606 ASN cc_start: 0.7767 (t0) cc_final: 0.7197 (t0) REVERT: A 616 ASN cc_start: 0.5866 (m110) cc_final: 0.5458 (m-40) REVERT: A 643 PHE cc_start: 0.5985 (t80) cc_final: 0.5697 (t80) REVERT: A 656 VAL cc_start: 0.7683 (p) cc_final: 0.7191 (t) REVERT: A 699 LEU cc_start: 0.4895 (OUTLIER) cc_final: 0.4673 (pp) REVERT: A 712 ILE cc_start: 0.8237 (pt) cc_final: 0.7919 (tp) REVERT: A 774 GLN cc_start: 0.7546 (mp10) cc_final: 0.7342 (mp10) REVERT: A 1109 PHE cc_start: 0.5986 (t80) cc_final: 0.5423 (t80) REVERT: D 41 ARG cc_start: 0.6515 (mtm110) cc_final: 0.6016 (mtm180) outliers start: 39 outliers final: 24 residues processed: 155 average time/residue: 0.1819 time to fit residues: 40.9481 Evaluate side-chains 144 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 449 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 726 ILE 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 916 LEU Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4719 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9253 Z= 0.213 Angle : 0.828 14.752 12584 Z= 0.430 Chirality : 0.049 0.284 1427 Planarity : 0.006 0.108 1636 Dihedral : 7.444 63.381 1254 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.34 % Favored : 84.14 % Rotamer: Outliers : 3.08 % Allowed : 18.81 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.23), residues: 1154 helix: -0.46 (0.34), residues: 201 sheet: -2.29 (0.35), residues: 196 loop : -3.27 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 107 HIS 0.003 0.001 HIS A 655 PHE 0.023 0.002 PHE A 338 TYR 0.038 0.002 TYR A 91 ARG 0.011 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7098 (t80) cc_final: 0.6878 (t80) REVERT: A 182 LYS cc_start: 0.0848 (OUTLIER) cc_final: 0.0007 (tttm) REVERT: A 307 THR cc_start: 0.7176 (m) cc_final: 0.6931 (m) REVERT: A 606 ASN cc_start: 0.7949 (t0) cc_final: 0.7140 (t0) REVERT: A 616 ASN cc_start: 0.5904 (m110) cc_final: 0.5460 (m-40) REVERT: A 643 PHE cc_start: 0.5930 (t80) cc_final: 0.5646 (t80) REVERT: A 656 VAL cc_start: 0.7554 (p) cc_final: 0.7107 (t) REVERT: A 699 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4809 (pp) REVERT: A 712 ILE cc_start: 0.8101 (pt) cc_final: 0.7832 (tp) REVERT: A 1095 PHE cc_start: 0.4548 (t80) cc_final: 0.4238 (t80) REVERT: A 1109 PHE cc_start: 0.5900 (t80) cc_final: 0.5313 (t80) REVERT: D 41 ARG cc_start: 0.6671 (mtm110) cc_final: 0.6272 (mtm180) REVERT: D 68 ARG cc_start: 0.6163 (mtt90) cc_final: 0.5958 (mtt90) REVERT: D 71 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8890 (tp) outliers start: 31 outliers final: 22 residues processed: 153 average time/residue: 0.1922 time to fit residues: 42.1366 Evaluate side-chains 150 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 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 449 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 582 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 888 PHE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL 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 33 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.0020 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.3188 ------------------------------------------------------------------------------- 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 928 ASN A 935 GLN A1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4672 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9253 Z= 0.205 Angle : 0.820 14.573 12584 Z= 0.422 Chirality : 0.049 0.248 1427 Planarity : 0.006 0.108 1636 Dihedral : 7.316 63.092 1254 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.21 % Favored : 85.27 % Rotamer: Outliers : 3.28 % Allowed : 19.50 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.23), residues: 1154 helix: -0.23 (0.34), residues: 201 sheet: -2.29 (0.35), residues: 196 loop : -3.23 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 107 HIS 0.002 0.001 HIS A 655 PHE 0.024 0.001 PHE A 906 TYR 0.024 0.002 TYR A 91 ARG 0.010 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6843 (t80) cc_final: 0.6631 (t80) REVERT: A 182 LYS cc_start: 0.0792 (OUTLIER) cc_final: -0.0103 (tttm) REVERT: A 307 THR cc_start: 0.7149 (m) cc_final: 0.6907 (m) REVERT: A 606 ASN cc_start: 0.8141 (t0) cc_final: 0.7610 (t0) REVERT: A 616 ASN cc_start: 0.6104 (m110) cc_final: 0.5622 (m-40) REVERT: A 656 VAL cc_start: 0.7569 (p) cc_final: 0.7107 (t) REVERT: A 699 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.4799 (pp) REVERT: A 712 ILE cc_start: 0.8081 (pt) cc_final: 0.7798 (tp) REVERT: A 938 LEU cc_start: 0.6038 (mp) cc_final: 0.5551 (mp) REVERT: A 1095 PHE cc_start: 0.4847 (t80) cc_final: 0.4481 (t80) REVERT: A 1109 PHE cc_start: 0.5853 (t80) cc_final: 0.5240 (t80) REVERT: D 31 SER cc_start: 0.6538 (OUTLIER) cc_final: 0.5656 (t) REVERT: D 41 ARG cc_start: 0.6695 (mtm110) cc_final: 0.6318 (mtm180) outliers start: 33 outliers final: 21 residues processed: 155 average time/residue: 0.1892 time to fit residues: 42.3913 Evaluate side-chains 144 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 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 402 ILE 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 699 LEU Chi-restraints excluded: chain A residue 726 ILE 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 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 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 107 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 94 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4708 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9253 Z= 0.212 Angle : 0.830 14.578 12584 Z= 0.428 Chirality : 0.049 0.242 1427 Planarity : 0.006 0.109 1636 Dihedral : 7.265 63.269 1254 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.61 % Allowed : 14.82 % Favored : 84.58 % Rotamer: Outliers : 3.28 % Allowed : 20.30 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.23), residues: 1154 helix: -0.17 (0.35), residues: 201 sheet: -2.24 (0.35), residues: 202 loop : -3.19 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 107 HIS 0.003 0.001 HIS A 655 PHE 0.027 0.002 PHE A 906 TYR 0.022 0.002 TYR A 91 ARG 0.011 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6743 (t80) cc_final: 0.6528 (t80) REVERT: A 182 LYS cc_start: 0.0659 (OUTLIER) cc_final: -0.0152 (tttm) REVERT: A 307 THR cc_start: 0.7149 (m) cc_final: 0.6898 (m) REVERT: A 602 THR cc_start: 0.6672 (OUTLIER) cc_final: 0.6430 (p) REVERT: A 606 ASN cc_start: 0.7987 (t0) cc_final: 0.7472 (t0) REVERT: A 616 ASN cc_start: 0.6095 (m110) cc_final: 0.5605 (m-40) REVERT: A 643 PHE cc_start: 0.6055 (t80) cc_final: 0.5748 (t80) REVERT: A 699 LEU cc_start: 0.5347 (OUTLIER) cc_final: 0.5105 (pp) REVERT: A 712 ILE cc_start: 0.8216 (pt) cc_final: 0.7896 (tp) REVERT: A 938 LEU cc_start: 0.6041 (mp) cc_final: 0.5733 (mp) REVERT: A 1095 PHE cc_start: 0.4886 (t80) cc_final: 0.4489 (t80) REVERT: D 41 ARG cc_start: 0.6723 (mtm110) cc_final: 0.6356 (mtm180) outliers start: 33 outliers final: 27 residues processed: 150 average time/residue: 0.1905 time to fit residues: 41.3422 Evaluate side-chains 150 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 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 367 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 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 699 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 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 Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 115 optimal weight: 0.0870 chunk 106 optimal weight: 0.0270 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.2980 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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 777 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4564 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9253 Z= 0.196 Angle : 0.810 14.707 12584 Z= 0.416 Chirality : 0.048 0.244 1427 Planarity : 0.006 0.107 1636 Dihedral : 7.020 62.090 1254 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.82 % Favored : 86.66 % Rotamer: Outliers : 2.69 % Allowed : 21.00 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.23), residues: 1154 helix: 0.05 (0.35), residues: 203 sheet: -2.12 (0.36), residues: 196 loop : -3.18 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 633 HIS 0.003 0.001 HIS A 655 PHE 0.026 0.001 PHE A 906 TYR 0.023 0.001 TYR A 91 ARG 0.012 0.001 ARG A1000 ********************** 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 154 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.0205 (OUTLIER) cc_final: -0.0628 (tttm) REVERT: A 307 THR cc_start: 0.7101 (m) cc_final: 0.6823 (m) REVERT: A 606 ASN cc_start: 0.8048 (t0) cc_final: 0.7545 (t0) REVERT: A 616 ASN cc_start: 0.6534 (m110) cc_final: 0.6236 (m-40) REVERT: A 712 ILE cc_start: 0.8349 (pt) cc_final: 0.8005 (tp) REVERT: A 1095 PHE cc_start: 0.4880 (t80) cc_final: 0.4493 (t80) REVERT: D 41 ARG cc_start: 0.6813 (mtm110) cc_final: 0.6546 (mtm180) outliers start: 27 outliers final: 21 residues processed: 152 average time/residue: 0.1985 time to fit residues: 43.9683 Evaluate side-chains 135 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 ILE 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 726 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 928 ASN Chi-restraints excluded: chain A residue 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 84 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1054 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5242 r_free = 0.5242 target = 0.309027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.275694 restraints weight = 18220.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.280981 restraints weight = 12448.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.284222 restraints weight = 9126.389| |-----------------------------------------------------------------------------| r_work (final): 0.5039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4413 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 9253 Z= 0.304 Angle : 1.054 59.199 12584 Z= 0.593 Chirality : 0.050 0.396 1427 Planarity : 0.006 0.108 1636 Dihedral : 7.023 61.939 1254 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.17 % Favored : 86.31 % Rotamer: Outliers : 2.89 % Allowed : 20.60 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.23), residues: 1154 helix: -0.14 (0.35), residues: 203 sheet: -2.10 (0.36), residues: 196 loop : -3.17 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 633 HIS 0.002 0.001 HIS A1064 PHE 0.044 0.002 PHE A 55 TYR 0.022 0.001 TYR A 91 ARG 0.015 0.001 ARG A1019 =============================================================================== Job complete usr+sys time: 2038.42 seconds wall clock time: 37 minutes 12.14 seconds (2232.14 seconds total)