Starting phenix.real_space_refine on Fri Dec 8 20:09:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/12_2023/7fg3_31577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/12_2023/7fg3_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_31577/12_2023/7fg3_31577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/12_2023/7fg3_31577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/12_2023/7fg3_31577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fg3_31577/12_2023/7fg3_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.00, 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: 3.49 Conformation dependent library (CDL) restraints added in 2.4 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: 0.97 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: 3.31 Time building geometry restraints manager: 4.04 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.920 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.280 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.390 ------------------------------------------------------------------------------- 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 : 0.957 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 outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1996 time to fit residues: 43.7332 Evaluate side-chains 126 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4681 ------------------------------------------------------------------------------- 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: 0.9980 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: 9.9990 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: 0.4723 moved from start: 0.1790 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= 0.243 Angle : 0.880 13.071 12584 Z= 0.471 Chirality : 0.051 0.261 1427 Planarity : 0.007 0.109 1636 Dihedral : 8.508 63.841 1254 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 27.34 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.68 % Favored : 83.62 % Rotamer: Outliers : 1.89 % Allowed : 11.84 % Favored : 86.27 % 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: -1.32 (0.33), residues: 198 sheet: -2.52 (0.35), residues: 174 loop : -3.52 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.013 0.002 HIS A1088 PHE 0.041 0.002 PHE A 823 TYR 0.017 0.002 TYR A 449 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 160 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 149 average time/residue: 0.2031 time to fit residues: 43.3187 Evaluate side-chains 142 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1121 time to fit residues: 3.9053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 165 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4754 moved from start: 0.2580 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= 0.226 Angle : 0.836 13.429 12584 Z= 0.444 Chirality : 0.050 0.243 1427 Planarity : 0.006 0.113 1636 Dihedral : 8.006 65.274 1254 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.55 % Favored : 82.84 % Rotamer: Outliers : 2.19 % Allowed : 14.83 % 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: -0.93 (0.33), residues: 204 sheet: -2.31 (0.34), residues: 196 loop : -3.50 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.005 0.001 HIS A 207 PHE 0.026 0.002 PHE A 823 TYR 0.025 0.002 TYR A 449 ARG 0.012 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 152 average time/residue: 0.1931 time to fit residues: 42.2589 Evaluate side-chains 131 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0848 time to fit residues: 2.8907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4834 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9253 Z= 0.265 Angle : 0.863 12.630 12584 Z= 0.453 Chirality : 0.050 0.260 1427 Planarity : 0.006 0.113 1636 Dihedral : 7.947 63.307 1254 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.72 % Favored : 82.67 % Rotamer: Outliers : 3.48 % Allowed : 16.72 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % 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: -4.05 (0.22), residues: 1154 helix: -0.88 (0.33), residues: 205 sheet: -2.50 (0.34), residues: 194 loop : -3.51 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 353 HIS 0.004 0.001 HIS A 207 PHE 0.040 0.002 PHE A 275 TYR 0.018 0.002 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 154 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 144 average time/residue: 0.2069 time to fit residues: 42.7182 Evaluate side-chains 128 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.883 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0927 time to fit residues: 3.6552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 1 optimal weight: 0.0060 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 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** ** A1083 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: 0.4761 moved from start: 0.3541 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= 0.219 Angle : 0.842 13.549 12584 Z= 0.439 Chirality : 0.050 0.230 1427 Planarity : 0.006 0.112 1636 Dihedral : 7.676 62.378 1254 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.12 % Favored : 83.36 % Rotamer: Outliers : 2.49 % Allowed : 18.81 % Favored : 78.71 % 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: -3.85 (0.23), residues: 1154 helix: -0.60 (0.35), residues: 199 sheet: -2.21 (0.36), residues: 193 loop : -3.44 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.003 0.001 HIS A1048 PHE 0.027 0.002 PHE A 275 TYR 0.018 0.001 TYR A 873 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 150 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 148 average time/residue: 0.1899 time to fit residues: 41.2549 Evaluate side-chains 126 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0887 time to fit residues: 3.3992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN ** 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 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** A 777 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** D 75 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4760 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9253 Z= 0.225 Angle : 0.818 14.129 12584 Z= 0.425 Chirality : 0.049 0.220 1427 Planarity : 0.006 0.114 1636 Dihedral : 7.543 62.238 1254 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 25.55 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.20 % Favored : 83.28 % Rotamer: Outliers : 1.59 % Allowed : 20.90 % Favored : 77.51 % 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: -3.79 (0.23), residues: 1154 helix: -0.53 (0.35), residues: 201 sheet: -2.14 (0.36), residues: 194 loop : -3.43 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS A1048 PHE 0.022 0.002 PHE A 275 TYR 0.016 0.002 TYR A 873 ARG 0.010 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 138 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 136 average time/residue: 0.2050 time to fit residues: 40.4559 Evaluate side-chains 123 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0879 time to fit residues: 2.7785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.0170 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 111 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 658 ASN ** 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** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4726 moved from start: 0.4273 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= 0.215 Angle : 0.835 18.538 12584 Z= 0.428 Chirality : 0.049 0.277 1427 Planarity : 0.006 0.115 1636 Dihedral : 7.467 60.939 1254 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 25.16 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.20 % Favored : 83.28 % Rotamer: Outliers : 1.29 % Allowed : 21.39 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.92 % Twisted General : 0.90 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.23), residues: 1154 helix: -0.55 (0.34), residues: 204 sheet: -2.03 (0.36), residues: 193 loop : -3.44 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 107 HIS 0.004 0.001 HIS A1048 PHE 0.024 0.002 PHE A 338 TYR 0.037 0.002 TYR A 91 ARG 0.009 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 127 average time/residue: 0.2033 time to fit residues: 37.0012 Evaluate side-chains 115 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0936 time to fit residues: 2.0996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.0570 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 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 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** 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: 0.4732 moved from start: 0.4618 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= 0.216 Angle : 0.818 14.804 12584 Z= 0.422 Chirality : 0.048 0.282 1427 Planarity : 0.006 0.115 1636 Dihedral : 7.335 59.799 1254 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.51 % Favored : 83.88 % Rotamer: Outliers : 1.39 % Allowed : 21.39 % Favored : 77.21 % 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: -3.73 (0.22), residues: 1154 helix: -0.53 (0.33), residues: 209 sheet: -2.03 (0.36), residues: 192 loop : -3.42 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 107 HIS 0.003 0.001 HIS A1048 PHE 0.019 0.002 PHE A 275 TYR 0.022 0.001 TYR A 91 ARG 0.006 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 127 average time/residue: 0.2309 time to fit residues: 41.8925 Evaluate side-chains 120 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0935 time to fit residues: 2.8386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 0.0370 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN A1010 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4833 moved from start: 0.4931 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= 0.261 Angle : 0.886 14.204 12584 Z= 0.461 Chirality : 0.050 0.292 1427 Planarity : 0.006 0.116 1636 Dihedral : 7.511 59.779 1254 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 28.57 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.64 % Favored : 82.76 % Rotamer: Outliers : 0.70 % Allowed : 22.09 % Favored : 77.21 % 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: -3.75 (0.22), residues: 1154 helix: -0.61 (0.33), residues: 208 sheet: -2.08 (0.36), residues: 197 loop : -3.40 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 107 HIS 0.005 0.001 HIS A 655 PHE 0.049 0.002 PHE A 275 TYR 0.022 0.002 TYR A1067 ARG 0.009 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 123 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 119 average time/residue: 0.2050 time to fit residues: 35.4240 Evaluate side-chains 112 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0840 time to fit residues: 1.8052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.0050 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 658 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4748 moved from start: 0.5189 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= 0.223 Angle : 0.850 14.925 12584 Z= 0.438 Chirality : 0.049 0.263 1427 Planarity : 0.006 0.115 1636 Dihedral : 7.344 56.592 1254 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.99 % Favored : 84.49 % Rotamer: Outliers : 0.20 % Allowed : 22.89 % Favored : 76.92 % 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: -3.73 (0.22), residues: 1154 helix: -0.63 (0.33), residues: 209 sheet: -1.97 (0.37), residues: 186 loop : -3.40 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 107 HIS 0.012 0.001 HIS A 655 PHE 0.053 0.002 PHE A 275 TYR 0.025 0.002 TYR A 91 ARG 0.010 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 118 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 0.2064 time to fit residues: 34.7245 Evaluate side-chains 113 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1017 time to fit residues: 1.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 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 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 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5199 r_free = 0.5199 target = 0.302676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.264572 restraints weight = 18734.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.270306 restraints weight = 12685.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.274437 restraints weight = 9410.113| |-----------------------------------------------------------------------------| r_work (final): 0.4981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4627 moved from start: 0.5539 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= 0.225 Angle : 0.855 15.450 12584 Z= 0.440 Chirality : 0.049 0.269 1427 Planarity : 0.006 0.115 1636 Dihedral : 7.259 56.954 1254 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 24.71 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.25 % Favored : 84.23 % Rotamer: Outliers : 0.10 % Allowed : 23.28 % Favored : 76.62 % 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: -3.68 (0.23), residues: 1154 helix: -0.51 (0.34), residues: 208 sheet: -1.96 (0.37), residues: 194 loop : -3.39 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 107 HIS 0.004 0.001 HIS A1048 PHE 0.046 0.002 PHE A 275 TYR 0.021 0.002 TYR A 91 ARG 0.007 0.001 ARG A 765 =============================================================================== Job complete usr+sys time: 2064.89 seconds wall clock time: 38 minutes 30.14 seconds (2310.14 seconds total)