Starting phenix.real_space_refine on Thu Mar 14 14:16:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/03_2024/7fg3_31577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/03_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_31577/03_2024/7fg3_31577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/03_2024/7fg3_31577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/03_2024/7fg3_31577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/03_2024/7fg3_31577.pdb" } 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 Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.02, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 3.63 Conformation dependent library (CDL) restraints added in 1.7 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 20 sheets defined 19.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 338 through 344 removed outlier: 4.104A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 416 through 422 removed outlier: 4.115A pdb=" N ASP A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.036A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 898 through 908 Processing helix chain 'A' and resid 913 through 941 removed outlier: 7.238A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.514A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.661A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.524A pdb=" N ASP D 91 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR D 92 " --> pdb=" O PRO D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.559A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.919A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 237 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.199A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.106A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.811A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.946A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.016A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.606A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.625A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 644 through 645 removed outlier: 3.654A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 670 through 671 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 721 removed outlier: 3.963A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 721 removed outlier: 3.963A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A1063 " --> pdb=" O PHE A1052 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A1065 " --> pdb=" O MET A1050 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.132A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A1088 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A1083 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.559A pdb=" N LEU D 19 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 12 through 13 removed outlier: 3.543A pdb=" N THR D 111 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 38 through 39 removed outlier: 3.617A pdb=" N ARG D 39 " --> pdb=" O GLU D 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 73 through 74 removed outlier: 3.806A pdb=" N ASP D 74 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR D 79 " --> pdb=" O ASP D 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 244 hydrogen bonds defined for protein. 672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 3.89 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: 93.55 - 102.13: 30 102.13 - 110.70: 2789 110.70 - 119.27: 4717 119.27 - 127.85: 4996 127.85 - 136.42: 52 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 2.440 nonbonded pdb=" NH1 ARG A 577 " pdb=" OD1 ASP A 578 " model vdw 2.019 2.520 nonbonded pdb=" O ASN A 710 " pdb=" OG1 THR A1077 " model vdw 2.035 2.440 nonbonded pdb=" OE2 GLU A 298 " pdb=" OG1 THR A 315 " model vdw 2.050 2.440 nonbonded pdb=" NE2 GLN A 321 " pdb=" O PRO A 621 " model vdw 2.075 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.860 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.860 Find NCS groups from input model: 0.260 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- 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 : 0.855 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: 0.2054 time to fit residues: 44.8125 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: 0.5980 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 282 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4720 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9253 Z= 0.241 Angle : 0.877 13.139 12584 Z= 0.470 Chirality : 0.052 0.271 1427 Planarity : 0.007 0.108 1636 Dihedral : 8.488 63.871 1254 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.94 % Favored : 83.36 % Rotamer: Outliers : 1.59 % Allowed : 11.64 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.90 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.22), residues: 1154 helix: -1.31 (0.33), residues: 198 sheet: -2.52 (0.35), residues: 175 loop : -3.52 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 107 HIS 0.008 0.002 HIS A1088 PHE 0.040 0.002 PHE A 823 TYR 0.022 0.002 TYR A 204 ARG 0.005 0.001 ARG A 466 *********************** 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 fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.0790 (mmt) cc_final: 0.0205 (mmt) REVERT: A 200 TYR cc_start: 0.3287 (t80) cc_final: 0.1812 (m-80) REVERT: A 303 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5288 (mp) REVERT: A 307 THR cc_start: 0.7397 (m) cc_final: 0.7128 (m) REVERT: A 656 VAL cc_start: 0.7702 (p) cc_final: 0.7222 (t) REVERT: A 1109 PHE cc_start: 0.5844 (t80) cc_final: 0.5278 (t80) outliers start: 16 outliers final: 10 residues processed: 151 average time/residue: 0.1989 time to fit residues: 42.3989 Evaluate side-chains 137 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 735 SER 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 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 0.4750 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9253 Z= 0.223 Angle : 0.824 13.286 12584 Z= 0.439 Chirality : 0.049 0.219 1427 Planarity : 0.006 0.112 1636 Dihedral : 8.013 64.349 1254 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.46 % Favored : 82.93 % Rotamer: Outliers : 2.79 % Allowed : 14.23 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.90 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.22), residues: 1154 helix: -0.95 (0.33), residues: 204 sheet: -2.34 (0.34), residues: 195 loop : -3.48 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 64 HIS 0.005 0.001 HIS A1088 PHE 0.029 0.002 PHE A 823 TYR 0.022 0.002 TYR A 449 ARG 0.004 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.891 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: 0.7817 (OUTLIER) cc_final: 0.7441 (mp) REVERT: A 303 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5530 (mm) REVERT: A 307 THR cc_start: 0.7200 (m) cc_final: 0.6940 (m) REVERT: A 740 MET cc_start: 0.6020 (tpt) cc_final: 0.5768 (tpt) REVERT: A 1109 PHE cc_start: 0.5842 (t80) cc_final: 0.5284 (t80) REVERT: D 68 ARG cc_start: 0.7279 (mtt-85) cc_final: 0.6736 (mpt-90) outliers start: 28 outliers final: 15 residues processed: 151 average time/residue: 0.1860 time to fit residues: 40.4129 Evaluate side-chains 140 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 312 ILE 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 487 ASN Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 916 LEU 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 104 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4768 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9253 Z= 0.225 Angle : 0.821 13.044 12584 Z= 0.431 Chirality : 0.049 0.215 1427 Planarity : 0.006 0.112 1636 Dihedral : 7.772 64.094 1254 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.69 % Allowed : 16.03 % Favored : 83.28 % Rotamer: Outliers : 4.58 % Allowed : 14.73 % Favored : 80.70 % 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: -3.87 (0.23), residues: 1154 helix: -0.66 (0.34), residues: 199 sheet: -2.37 (0.35), residues: 190 loop : -3.40 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 107 HIS 0.004 0.001 HIS A 207 PHE 0.035 0.002 PHE A 275 TYR 0.019 0.001 TYR A 449 ARG 0.007 0.001 ARG A 765 *********************** 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 173 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.5069 (mm) REVERT: A 307 THR cc_start: 0.7068 (m) cc_final: 0.6844 (m) REVERT: A 402 ILE cc_start: 0.6078 (OUTLIER) cc_final: 0.5675 (tt) REVERT: A 542 ASN cc_start: 0.4648 (t0) cc_final: 0.4138 (t0) REVERT: A 656 VAL cc_start: 0.7772 (p) cc_final: 0.7181 (t) REVERT: A 740 MET cc_start: 0.6139 (tpt) cc_final: 0.5910 (tpt) REVERT: A 1109 PHE cc_start: 0.5840 (t80) cc_final: 0.5282 (t80) REVERT: D 41 ARG cc_start: 0.6558 (mtm110) cc_final: 0.5989 (mtm180) REVERT: D 68 ARG cc_start: 0.7099 (mtt-85) cc_final: 0.6569 (mpt-90) outliers start: 46 outliers final: 22 residues processed: 159 average time/residue: 0.2021 time to fit residues: 46.4659 Evaluate side-chains 146 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 449 TYR 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 487 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 861 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 0.0000 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 0.0270 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4821 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9253 Z= 0.239 Angle : 0.830 13.034 12584 Z= 0.435 Chirality : 0.049 0.246 1427 Planarity : 0.006 0.114 1636 Dihedral : 7.645 61.943 1254 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.90 % Favored : 82.58 % Rotamer: Outliers : 4.38 % Allowed : 17.91 % Favored : 77.71 % 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: -3.90 (0.23), residues: 1154 helix: -0.76 (0.34), residues: 206 sheet: -2.32 (0.34), residues: 193 loop : -3.44 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 64 HIS 0.004 0.001 HIS A 655 PHE 0.027 0.002 PHE A 275 TYR 0.020 0.002 TYR A 449 ARG 0.008 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 163 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 119 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5394 (mm) REVERT: A 576 VAL cc_start: 0.1105 (OUTLIER) cc_final: 0.0836 (p) REVERT: A 606 ASN cc_start: 0.7735 (t0) cc_final: 0.7215 (t0) REVERT: A 656 VAL cc_start: 0.7787 (p) cc_final: 0.7295 (t) REVERT: A 740 MET cc_start: 0.6089 (tpt) cc_final: 0.5877 (tpt) REVERT: A 936 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6888 (t70) REVERT: A 1095 PHE cc_start: 0.4266 (t80) cc_final: 0.3859 (t80) REVERT: A 1109 PHE cc_start: 0.6166 (t80) cc_final: 0.5646 (t80) REVERT: D 4 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7832 (tp-100) REVERT: D 41 ARG cc_start: 0.6605 (mtm110) cc_final: 0.6194 (mtm180) REVERT: D 68 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6559 (mpt-90) outliers start: 44 outliers final: 28 residues processed: 155 average time/residue: 0.1807 time to fit residues: 40.7195 Evaluate side-chains 147 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 THR 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 487 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 735 SER 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 936 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** 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: 0.4827 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9253 Z= 0.241 Angle : 0.822 13.299 12584 Z= 0.432 Chirality : 0.049 0.239 1427 Planarity : 0.006 0.113 1636 Dihedral : 7.529 62.648 1254 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.98 % Favored : 82.50 % Rotamer: Outliers : 4.08 % Allowed : 18.51 % Favored : 77.41 % 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: -3.86 (0.23), residues: 1154 helix: -0.74 (0.34), residues: 206 sheet: -2.24 (0.35), residues: 188 loop : -3.42 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.003 0.001 HIS A 655 PHE 0.022 0.002 PHE A 275 TYR 0.017 0.002 TYR A 449 ARG 0.009 0.001 ARG A 765 *********************** 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 159 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 118 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 303 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5341 (mm) REVERT: A 321 GLN cc_start: 0.4215 (OUTLIER) cc_final: 0.3834 (tp-100) REVERT: A 406 GLU cc_start: 0.6592 (tm-30) cc_final: 0.6266 (tm-30) REVERT: A 576 VAL cc_start: 0.1080 (OUTLIER) cc_final: 0.0763 (p) REVERT: A 606 ASN cc_start: 0.7942 (t0) cc_final: 0.7319 (t0) REVERT: A 656 VAL cc_start: 0.7782 (p) cc_final: 0.7350 (t) REVERT: A 900 MET cc_start: 0.0691 (mmp) cc_final: 0.0475 (mmm) REVERT: A 936 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6857 (t70) REVERT: A 1095 PHE cc_start: 0.4164 (t80) cc_final: 0.3790 (t80) REVERT: A 1109 PHE cc_start: 0.6235 (t80) cc_final: 0.5734 (t80) REVERT: D 68 ARG cc_start: 0.7044 (mtt-85) cc_final: 0.6568 (mpt-90) outliers start: 41 outliers final: 29 residues processed: 152 average time/residue: 0.1841 time to fit residues: 40.5281 Evaluate side-chains 149 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 450 ASN 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 487 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 936 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 66 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 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 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4738 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9253 Z= 0.206 Angle : 0.784 13.964 12584 Z= 0.409 Chirality : 0.047 0.205 1427 Planarity : 0.006 0.113 1636 Dihedral : 7.245 61.695 1254 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 22.64 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.90 % Favored : 84.58 % Rotamer: Outliers : 3.88 % Allowed : 19.50 % Favored : 76.62 % 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: -3.68 (0.23), residues: 1154 helix: -0.41 (0.35), residues: 199 sheet: -2.11 (0.36), residues: 191 loop : -3.34 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 107 HIS 0.005 0.001 HIS A1048 PHE 0.026 0.002 PHE A 338 TYR 0.018 0.001 TYR A 873 ARG 0.003 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 164 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5640 (mm) REVERT: A 321 GLN cc_start: 0.4192 (OUTLIER) cc_final: 0.3671 (tp-100) REVERT: A 406 GLU cc_start: 0.6509 (tm-30) cc_final: 0.6268 (tm-30) REVERT: A 576 VAL cc_start: 0.1208 (OUTLIER) cc_final: 0.0866 (p) REVERT: A 606 ASN cc_start: 0.8183 (t0) cc_final: 0.7650 (t0) REVERT: A 936 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6716 (t70) REVERT: A 1095 PHE cc_start: 0.4312 (t80) cc_final: 0.3840 (t80) REVERT: D 31 SER cc_start: 0.6749 (m) cc_final: 0.6200 (t) outliers start: 39 outliers final: 25 residues processed: 157 average time/residue: 0.1954 time to fit residues: 44.4912 Evaluate side-chains 145 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN 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 615 VAL Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 360 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** 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: 0.4720 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9253 Z= 0.199 Angle : 0.792 14.521 12584 Z= 0.411 Chirality : 0.048 0.202 1427 Planarity : 0.006 0.113 1636 Dihedral : 7.147 60.091 1254 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.99 % Favored : 84.49 % Rotamer: Outliers : 4.18 % Allowed : 20.40 % Favored : 75.42 % 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: -3.59 (0.23), residues: 1154 helix: -0.32 (0.35), residues: 201 sheet: -2.03 (0.36), residues: 185 loop : -3.29 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 107 HIS 0.005 0.001 HIS A 655 PHE 0.017 0.001 PHE A 275 TYR 0.018 0.001 TYR A 873 ARG 0.007 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 158 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 0.911 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: 0.1623 (OUTLIER) cc_final: 0.0357 (tmtt) REVERT: A 303 LEU cc_start: 0.5694 (OUTLIER) cc_final: 0.5351 (mm) REVERT: A 321 GLN cc_start: 0.4328 (OUTLIER) cc_final: 0.2843 (tp-100) REVERT: A 449 TYR cc_start: 0.4623 (OUTLIER) cc_final: 0.4417 (t80) REVERT: A 576 VAL cc_start: 0.0704 (OUTLIER) cc_final: 0.0336 (p) REVERT: A 606 ASN cc_start: 0.8049 (t0) cc_final: 0.7574 (t0) REVERT: A 1095 PHE cc_start: 0.4540 (t80) cc_final: 0.4245 (t80) REVERT: D 31 SER cc_start: 0.6808 (m) cc_final: 0.6248 (t) REVERT: D 68 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6786 (mtt90) outliers start: 42 outliers final: 29 residues processed: 152 average time/residue: 0.1860 time to fit residues: 40.9530 Evaluate side-chains 149 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 450 ASN 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 597 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 805 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 1005 GLN Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 58 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4894 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9253 Z= 0.275 Angle : 0.858 15.509 12584 Z= 0.451 Chirality : 0.050 0.200 1427 Planarity : 0.006 0.116 1636 Dihedral : 7.456 60.946 1254 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 28.96 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.98 % Favored : 82.41 % Rotamer: Outliers : 3.68 % Allowed : 21.09 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.23), residues: 1154 helix: -0.46 (0.34), residues: 197 sheet: -2.19 (0.35), residues: 197 loop : -3.37 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 107 HIS 0.006 0.001 HIS A 655 PHE 0.019 0.002 PHE A 275 TYR 0.022 0.002 TYR A 449 ARG 0.010 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 157 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.1407 (OUTLIER) cc_final: 0.0169 (tmtt) REVERT: A 275 PHE cc_start: 0.1086 (OUTLIER) cc_final: 0.0829 (m-80) REVERT: A 321 GLN cc_start: 0.4660 (OUTLIER) cc_final: 0.4240 (tp-100) REVERT: A 606 ASN cc_start: 0.8015 (t0) cc_final: 0.7433 (t0) REVERT: A 643 PHE cc_start: 0.6063 (t80) cc_final: 0.5694 (t80) REVERT: A 819 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 938 LEU cc_start: 0.6447 (mp) cc_final: 0.6073 (mp) REVERT: A 1095 PHE cc_start: 0.4521 (t80) cc_final: 0.4120 (t80) REVERT: D 31 SER cc_start: 0.6706 (m) cc_final: 0.6107 (t) REVERT: D 68 ARG cc_start: 0.6987 (mtt-85) cc_final: 0.6442 (mpt-90) outliers start: 37 outliers final: 27 residues processed: 151 average time/residue: 0.1820 time to fit residues: 39.9585 Evaluate side-chains 148 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN 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 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 805 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL 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: 2.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 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 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4806 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9253 Z= 0.222 Angle : 0.829 16.758 12584 Z= 0.427 Chirality : 0.049 0.218 1427 Planarity : 0.006 0.114 1636 Dihedral : 7.316 58.349 1254 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.08 % Favored : 84.32 % Rotamer: Outliers : 2.89 % Allowed : 22.39 % Favored : 74.73 % 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: -3.66 (0.23), residues: 1154 helix: -0.37 (0.35), residues: 198 sheet: -2.06 (0.36), residues: 186 loop : -3.33 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.005 0.001 HIS A 655 PHE 0.020 0.002 PHE A 275 TYR 0.020 0.001 TYR A 449 ARG 0.009 0.001 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.0822 (OUTLIER) cc_final: -0.0322 (tmtt) REVERT: A 275 PHE cc_start: 0.0937 (OUTLIER) cc_final: 0.0736 (m-80) REVERT: A 321 GLN cc_start: 0.4544 (OUTLIER) cc_final: 0.3878 (tp-100) REVERT: A 643 PHE cc_start: 0.5938 (t80) cc_final: 0.5580 (t80) REVERT: A 819 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 1095 PHE cc_start: 0.4440 (t80) cc_final: 0.3961 (t80) REVERT: D 31 SER cc_start: 0.6725 (m) cc_final: 0.6118 (t) REVERT: D 68 ARG cc_start: 0.7029 (mtt-85) cc_final: 0.6345 (mpt-90) outliers start: 29 outliers final: 26 residues processed: 139 average time/residue: 0.1950 time to fit residues: 38.9083 Evaluate side-chains 140 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 182 LYS Chi-restraints excluded: chain A residue 227 VAL 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 367 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ASN 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 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1067 TYR Chi-restraints excluded: chain D residue 6 VAL 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 84 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.0030 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 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 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5179 r_free = 0.5179 target = 0.301025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.261814 restraints weight = 17914.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.266857 restraints weight = 12889.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.270568 restraints weight = 9376.937| |-----------------------------------------------------------------------------| r_work (final): 0.4948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4691 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9253 Z= 0.219 Angle : 0.831 16.613 12584 Z= 0.430 Chirality : 0.048 0.220 1427 Planarity : 0.006 0.114 1636 Dihedral : 7.226 57.777 1254 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.42 % Favored : 83.97 % Rotamer: Outliers : 3.48 % Allowed : 22.29 % Favored : 74.23 % 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: -3.68 (0.23), residues: 1154 helix: -0.52 (0.34), residues: 206 sheet: -1.99 (0.36), residues: 186 loop : -3.36 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 107 HIS 0.004 0.001 HIS A 655 PHE 0.018 0.002 PHE A 275 TYR 0.022 0.001 TYR A 508 ARG 0.010 0.001 ARG A 765 =============================================================================== Job complete usr+sys time: 1964.31 seconds wall clock time: 36 minutes 26.12 seconds (2186.12 seconds total)