Starting phenix.real_space_refine on Thu Nov 14 00:36:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/11_2024/8owe_17235.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/11_2024/8owe_17235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/11_2024/8owe_17235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/11_2024/8owe_17235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/11_2024/8owe_17235.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owe_17235/11_2024/8owe_17235.cif" } resolution = 3.75 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.001 sd= 0.006 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 10 5.16 5 C 1880 2.51 5 N 515 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2940 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 283 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Restraints were copied for chains: F, I, H, J, C, B, E, D Time building chain proxies: 1.71, per 1000 atoms: 0.58 Number of scatterers: 2940 At special positions: 0 Unit cell: (79.8, 106.05, 50.4, 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 10 16.00 O 535 8.00 N 515 7.00 C 1880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 426.1 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 46.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.116A pdb=" N TYR A 10 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR B 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR C 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR D 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 23 Processing sheet with id=AA3, first strand: chain 'F' and resid 2 through 23 removed outlier: 8.867A pdb=" N ALA F 2 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N ARG G 5 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE F 4 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ASP G 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N HIS F 6 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N GLY G 9 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER F 8 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU G 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR F 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS G 13 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL F 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN G 15 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N HIS F 14 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N LEU G 17 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS F 16 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N PHE G 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL F 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N ALA G 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N PHE F 20 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ASP G 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU F 22 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA G 2 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N ARG H 5 " --> pdb=" O ALA G 2 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE G 4 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N ASP H 7 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N HIS G 6 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N GLY H 9 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER G 8 " --> pdb=" O GLY H 9 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU H 11 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR G 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS H 13 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL G 12 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN H 15 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N HIS G 14 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N LEU H 17 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS G 16 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N PHE H 19 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL G 18 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N ALA H 21 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N PHE G 20 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ASP H 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU G 22 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA H 2 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N ARG I 5 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE H 4 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N ASP I 7 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N HIS H 6 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 9.918A pdb=" N GLY I 9 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N SER H 8 " --> pdb=" O GLY I 9 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU I 11 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR H 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS I 13 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL H 12 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN I 15 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N HIS H 14 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N LEU I 17 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS H 16 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N PHE I 19 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL H 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N ALA I 21 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N PHE H 20 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ASP I 23 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU H 22 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA I 2 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N ARG J 5 " --> pdb=" O ALA I 2 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N PHE I 4 " --> pdb=" O ARG J 5 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N ASP J 7 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N HIS I 6 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N GLY J 9 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER I 8 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU J 11 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR I 10 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS J 13 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL I 12 " --> pdb=" O HIS J 13 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN J 15 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N HIS I 14 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 10.081A pdb=" N LEU J 17 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS I 16 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N PHE J 19 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N VAL I 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ALA J 21 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N PHE I 20 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 10.335A pdb=" N ASP J 23 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLU I 22 " --> pdb=" O ASP J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 29 through 36 removed outlier: 6.784A pdb=" N ALA G 30 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE F 31 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE G 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY F 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA H 30 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE G 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE H 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY G 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA I 30 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE H 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE I 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY H 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA J 30 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE I 31 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE J 32 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY I 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 120 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: 0.62 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 819 1.33 - 1.45: 560 1.45 - 1.57: 1587 1.57 - 1.69: 14 1.69 - 1.81: 20 Bond restraints: 3000 Sorted by residual: bond pdb=" CA MET J 35 " pdb=" C MET J 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.37e+01 bond pdb=" CA MET H 35 " pdb=" C MET H 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" CA MET F 35 " pdb=" C MET F 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" CA MET I 35 " pdb=" C MET I 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" CA MET G 35 " pdb=" C MET G 35 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.27e-02 6.20e+03 1.35e+01 ... (remaining 2995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 2432 1.80 - 3.60: 1073 3.60 - 5.40: 352 5.40 - 7.20: 95 7.20 - 9.00: 68 Bond angle restraints: 4020 Sorted by residual: angle pdb=" O ILE E 32 " pdb=" C ILE E 32 " pdb=" N GLY E 33 " ideal model delta sigma weight residual 122.76 114.63 8.13 1.04e+00 9.25e-01 6.11e+01 angle pdb=" O ILE D 32 " pdb=" C ILE D 32 " pdb=" N GLY D 33 " ideal model delta sigma weight residual 122.76 114.64 8.12 1.04e+00 9.25e-01 6.09e+01 angle pdb=" O ILE C 32 " pdb=" C ILE C 32 " pdb=" N GLY C 33 " ideal model delta sigma weight residual 122.76 114.66 8.10 1.04e+00 9.25e-01 6.07e+01 angle pdb=" O ILE A 32 " pdb=" C ILE A 32 " pdb=" N GLY A 33 " ideal model delta sigma weight residual 122.76 114.66 8.10 1.04e+00 9.25e-01 6.07e+01 angle pdb=" O ILE B 32 " pdb=" C ILE B 32 " pdb=" N GLY B 33 " ideal model delta sigma weight residual 122.76 114.68 8.08 1.04e+00 9.25e-01 6.03e+01 ... (remaining 4015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1395 17.40 - 34.79: 170 34.79 - 52.19: 60 52.19 - 69.58: 20 69.58 - 86.98: 25 Dihedral angle restraints: 1670 sinusoidal: 635 harmonic: 1035 Sorted by residual: dihedral pdb=" C VAL B 24 " pdb=" N VAL B 24 " pdb=" CA VAL B 24 " pdb=" CB VAL B 24 " ideal model delta harmonic sigma weight residual -122.00 -136.33 14.33 0 2.50e+00 1.60e-01 3.28e+01 dihedral pdb=" C VAL E 24 " pdb=" N VAL E 24 " pdb=" CA VAL E 24 " pdb=" CB VAL E 24 " ideal model delta harmonic sigma weight residual -122.00 -136.33 14.33 0 2.50e+00 1.60e-01 3.28e+01 dihedral pdb=" C VAL C 24 " pdb=" N VAL C 24 " pdb=" CA VAL C 24 " pdb=" CB VAL C 24 " ideal model delta harmonic sigma weight residual -122.00 -136.32 14.32 0 2.50e+00 1.60e-01 3.28e+01 ... (remaining 1667 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.096: 169 0.096 - 0.189: 175 0.189 - 0.281: 41 0.281 - 0.373: 20 0.373 - 0.465: 20 Chirality restraints: 425 Sorted by residual: chirality pdb=" CA VAL D 24 " pdb=" N VAL D 24 " pdb=" C VAL D 24 " pdb=" CB VAL D 24 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA VAL A 24 " pdb=" N VAL A 24 " pdb=" C VAL A 24 " pdb=" CB VAL A 24 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.40e+00 chirality pdb=" CA VAL B 24 " pdb=" N VAL B 24 " pdb=" C VAL B 24 " pdb=" CB VAL B 24 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 422 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 13 " 0.117 2.00e-02 2.50e+03 8.75e-02 1.15e+02 pdb=" CG HIS I 13 " -0.122 2.00e-02 2.50e+03 pdb=" ND1 HIS I 13 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 HIS I 13 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS I 13 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 HIS I 13 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS J 13 " 0.117 2.00e-02 2.50e+03 8.75e-02 1.15e+02 pdb=" CG HIS J 13 " -0.122 2.00e-02 2.50e+03 pdb=" ND1 HIS J 13 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 HIS J 13 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS J 13 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 HIS J 13 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 13 " 0.117 2.00e-02 2.50e+03 8.75e-02 1.15e+02 pdb=" CG HIS F 13 " -0.122 2.00e-02 2.50e+03 pdb=" ND1 HIS F 13 " -0.065 2.00e-02 2.50e+03 pdb=" CD2 HIS F 13 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS F 13 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 HIS F 13 " 0.062 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 7 2.44 - 3.06: 1812 3.06 - 3.67: 4609 3.67 - 4.29: 6852 4.29 - 4.90: 12265 Nonbonded interactions: 25545 Sorted by model distance: nonbonded pdb=" OD2 ASP B 7 " pdb=" NE ARG C 5 " model vdw 1.831 3.120 nonbonded pdb=" OD2 ASP C 7 " pdb=" NE ARG D 5 " model vdw 1.831 3.120 nonbonded pdb=" OD2 ASP A 7 " pdb=" NE ARG B 5 " model vdw 1.831 3.120 nonbonded pdb=" OD2 ASP D 7 " pdb=" NE ARG E 5 " model vdw 1.831 3.120 nonbonded pdb=" NE2 HIS A 14 " pdb=" OD2 ASP H 1 " model vdw 2.399 3.120 ... (remaining 25540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 4 through 40) selection = (chain 'G' and resid 4 through 40) selection = (chain 'H' and resid 4 through 40) selection = (chain 'I' and resid 4 through 40) selection = (chain 'J' and resid 4 through 40) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.014 0.056 3000 Z= 0.956 Angle : 2.465 9.004 4020 Z= 1.707 Chirality : 0.170 0.465 425 Planarity : 0.028 0.144 525 Dihedral : 22.521 86.977 1020 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 18.33 % Allowed : 13.33 % Favored : 68.33 % Cbeta Deviations : 6.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.67 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.023 0.010 HIS J 14 PHE 0.060 0.012 PHE J 19 TYR 0.024 0.010 TYR E 10 ARG 0.006 0.002 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7465 (tppt) REVERT: A 35 MET cc_start: 0.7941 (ptt) cc_final: 0.6000 (mmp) REVERT: E 31 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.7888 (tp) REVERT: F 28 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6723 (mmtm) REVERT: G 8 SER cc_start: 0.8545 (p) cc_final: 0.8150 (p) REVERT: H 39 VAL cc_start: 0.9128 (t) cc_final: 0.8743 (m) REVERT: H 40 VAL cc_start: 0.8571 (t) cc_final: 0.8361 (t) REVERT: J 16 LYS cc_start: 0.7706 (ttmt) cc_final: 0.7249 (mmmt) outliers start: 55 outliers final: 9 residues processed: 180 average time/residue: 0.1605 time to fit residues: 33.5515 Evaluate side-chains 106 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS F 6 HIS F 27 ASN G 6 HIS G 27 ASN H 6 HIS H 27 ASN I 6 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3000 Z= 0.308 Angle : 0.717 6.337 4020 Z= 0.401 Chirality : 0.052 0.165 425 Planarity : 0.004 0.017 525 Dihedral : 11.357 59.679 431 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 10.33 % Allowed : 20.00 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.26), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS E 13 PHE 0.019 0.002 PHE G 4 TYR 0.007 0.001 TYR E 10 ARG 0.003 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.351 Fit side-chains REVERT: A 28 LYS cc_start: 0.8831 (ptpt) cc_final: 0.7534 (tppt) REVERT: A 35 MET cc_start: 0.7393 (ptt) cc_final: 0.5332 (mmp) REVERT: B 12 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7575 (m) REVERT: B 22 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7650 (tp30) REVERT: D 22 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8052 (tm-30) REVERT: F 28 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6259 (mmtm) REVERT: G 23 ASP cc_start: 0.7123 (t0) cc_final: 0.6641 (t0) REVERT: G 27 ASN cc_start: 0.7292 (t0) cc_final: 0.7071 (t0) REVERT: G 28 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7730 (ptpt) REVERT: G 35 MET cc_start: 0.8210 (ttm) cc_final: 0.8002 (ttt) REVERT: H 23 ASP cc_start: 0.7378 (t0) cc_final: 0.6699 (t0) REVERT: J 13 HIS cc_start: 0.6472 (OUTLIER) cc_final: 0.5515 (t70) REVERT: J 23 ASP cc_start: 0.5848 (t0) cc_final: 0.5591 (t0) outliers start: 31 outliers final: 15 residues processed: 132 average time/residue: 0.1381 time to fit residues: 21.9193 Evaluate side-chains 111 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.0980 chunk 21 optimal weight: 9.9990 overall best weight: 6.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 HIS H 13 HIS J 6 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3000 Z= 0.488 Angle : 0.750 6.154 4020 Z= 0.419 Chirality : 0.050 0.160 425 Planarity : 0.004 0.027 525 Dihedral : 10.323 53.025 425 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 8.67 % Allowed : 27.00 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.50 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 13 PHE 0.016 0.003 PHE F 4 TYR 0.016 0.002 TYR E 10 ARG 0.003 0.001 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.351 Fit side-chains REVERT: A 28 LYS cc_start: 0.8541 (ptpt) cc_final: 0.7005 (tppt) REVERT: A 35 MET cc_start: 0.7486 (ptt) cc_final: 0.5247 (mmp) REVERT: B 22 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 13 HIS cc_start: 0.7727 (t-90) cc_final: 0.7471 (t70) REVERT: F 5 ARG cc_start: 0.7557 (ttp80) cc_final: 0.6884 (tpm170) REVERT: F 28 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.5686 (mtpp) REVERT: G 28 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7811 (ptpt) outliers start: 26 outliers final: 19 residues processed: 109 average time/residue: 0.1536 time to fit residues: 19.7143 Evaluate side-chains 102 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 HIS H 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.6666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3000 Z= 0.305 Angle : 0.654 6.145 4020 Z= 0.355 Chirality : 0.049 0.156 425 Planarity : 0.003 0.012 525 Dihedral : 9.704 49.865 425 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 8.33 % Allowed : 27.33 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.63 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS B 13 PHE 0.011 0.002 PHE J 19 TYR 0.010 0.001 TYR E 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.359 Fit side-chains REVERT: A 35 MET cc_start: 0.7261 (ptt) cc_final: 0.5022 (mmp) REVERT: B 22 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7869 (tm-30) REVERT: B 28 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8759 (mttp) REVERT: C 28 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8776 (ptpp) REVERT: D 11 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7860 (tp30) REVERT: F 28 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.5427 (mtpp) REVERT: G 28 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7862 (ptpt) REVERT: I 11 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7056 (tm-30) REVERT: J 23 ASP cc_start: 0.6386 (t0) cc_final: 0.4911 (p0) REVERT: J 28 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7345 (pttt) outliers start: 25 outliers final: 17 residues processed: 106 average time/residue: 0.1489 time to fit residues: 18.8196 Evaluate side-chains 105 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.7016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3000 Z= 0.335 Angle : 0.657 5.260 4020 Z= 0.353 Chirality : 0.049 0.149 425 Planarity : 0.003 0.017 525 Dihedral : 9.217 46.344 421 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 9.00 % Allowed : 27.00 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 13 PHE 0.013 0.002 PHE J 19 TYR 0.010 0.001 TYR E 10 ARG 0.002 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.318 Fit side-chains REVERT: A 35 MET cc_start: 0.7290 (ptt) cc_final: 0.5029 (mmp) REVERT: B 22 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7458 (tm-30) REVERT: B 28 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.9019 (ptpp) REVERT: D 13 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6721 (m-70) REVERT: F 28 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.5268 (mtpp) REVERT: G 28 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7939 (ptpt) REVERT: J 11 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6909 (tm-30) REVERT: J 23 ASP cc_start: 0.6438 (t0) cc_final: 0.6033 (t0) outliers start: 27 outliers final: 17 residues processed: 100 average time/residue: 0.1439 time to fit residues: 17.0410 Evaluate side-chains 101 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3000 Z= 0.262 Angle : 0.615 5.976 4020 Z= 0.324 Chirality : 0.049 0.150 425 Planarity : 0.003 0.011 525 Dihedral : 8.617 45.608 419 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 8.00 % Allowed : 27.00 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.72 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.010 0.002 PHE D 20 TYR 0.006 0.001 TYR E 10 ARG 0.001 0.000 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.364 Fit side-chains REVERT: A 35 MET cc_start: 0.7169 (ptt) cc_final: 0.4991 (mmp) REVERT: B 22 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 28 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8986 (ptpp) REVERT: D 11 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7618 (tp30) REVERT: D 13 HIS cc_start: 0.7438 (OUTLIER) cc_final: 0.6879 (m-70) REVERT: D 22 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8071 (tm-30) REVERT: F 28 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.5063 (mtpp) REVERT: G 28 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8076 (ptpt) REVERT: J 11 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7031 (tm-30) REVERT: J 23 ASP cc_start: 0.6427 (t0) cc_final: 0.6038 (t0) outliers start: 24 outliers final: 15 residues processed: 97 average time/residue: 0.1452 time to fit residues: 16.9678 Evaluate side-chains 97 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3000 Z= 0.257 Angle : 0.606 5.839 4020 Z= 0.322 Chirality : 0.049 0.150 425 Planarity : 0.003 0.015 525 Dihedral : 8.543 45.240 419 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 7.67 % Allowed : 28.33 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.009 0.002 PHE J 19 TYR 0.008 0.001 TYR C 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.352 Fit side-chains REVERT: A 35 MET cc_start: 0.7228 (ptt) cc_final: 0.5019 (mmp) REVERT: B 22 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 28 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.9048 (ptpp) REVERT: D 11 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7723 (tp30) REVERT: D 13 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6920 (m-70) REVERT: F 28 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.5044 (mtpp) REVERT: G 28 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8176 (ptpt) REVERT: J 11 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6871 (tm-30) REVERT: J 28 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7026 (pttt) outliers start: 23 outliers final: 17 residues processed: 93 average time/residue: 0.1355 time to fit residues: 15.2704 Evaluate side-chains 101 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.7529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3000 Z= 0.246 Angle : 0.619 6.568 4020 Z= 0.322 Chirality : 0.049 0.150 425 Planarity : 0.003 0.015 525 Dihedral : 8.401 45.391 419 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 8.33 % Allowed : 28.33 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.78 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 14 PHE 0.009 0.001 PHE D 20 TYR 0.007 0.001 TYR C 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.332 Fit side-chains REVERT: A 35 MET cc_start: 0.7207 (ptt) cc_final: 0.5017 (mmp) REVERT: B 22 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 28 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9106 (ptpp) REVERT: C 28 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8849 (ptpp) REVERT: D 11 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7817 (tp30) REVERT: D 13 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6932 (m-70) REVERT: D 22 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8167 (tm-30) REVERT: F 28 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.4834 (tppp) REVERT: G 28 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8139 (ptpt) REVERT: J 11 GLU cc_start: 0.7410 (tm-30) cc_final: 0.6952 (tm-30) REVERT: J 28 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6878 (pttt) outliers start: 25 outliers final: 17 residues processed: 97 average time/residue: 0.1471 time to fit residues: 17.2840 Evaluate side-chains 101 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 28 LYS Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.7649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3000 Z= 0.299 Angle : 0.643 6.585 4020 Z= 0.338 Chirality : 0.049 0.149 425 Planarity : 0.003 0.017 525 Dihedral : 8.501 44.744 419 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 8.00 % Allowed : 28.33 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 13 PHE 0.011 0.002 PHE J 19 TYR 0.010 0.001 TYR C 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.296 Fit side-chains REVERT: A 35 MET cc_start: 0.7432 (ptt) cc_final: 0.5014 (mmp) REVERT: B 11 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 22 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7429 (tm-30) REVERT: B 28 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9040 (ptpp) REVERT: D 11 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7791 (tp30) REVERT: D 13 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.6937 (m-70) REVERT: D 22 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8113 (tm-30) REVERT: F 28 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.4991 (mtpp) REVERT: G 28 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8037 (ptpt) REVERT: J 5 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7022 (pmt-80) REVERT: J 11 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6900 (tm-30) outliers start: 24 outliers final: 19 residues processed: 92 average time/residue: 0.1508 time to fit residues: 16.6255 Evaluate side-chains 100 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain J residue 5 ARG Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.7729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3000 Z= 0.268 Angle : 0.645 6.802 4020 Z= 0.336 Chirality : 0.049 0.148 425 Planarity : 0.003 0.017 525 Dihedral : 8.447 45.759 419 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 8.00 % Allowed : 28.33 % Favored : 63.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 14 PHE 0.009 0.002 PHE J 19 TYR 0.008 0.001 TYR C 10 ARG 0.001 0.000 ARG B 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.448 Fit side-chains REVERT: A 35 MET cc_start: 0.7568 (ptt) cc_final: 0.4964 (mmp) REVERT: B 11 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7404 (tm-30) REVERT: B 22 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7399 (tm-30) REVERT: B 28 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9034 (ptpp) REVERT: D 11 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: D 13 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.6959 (m-70) REVERT: D 22 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8112 (tm-30) REVERT: F 28 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.4987 (mtpp) REVERT: G 28 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7890 (ptpt) REVERT: J 11 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7000 (tm-30) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 0.1404 time to fit residues: 15.6300 Evaluate side-chains 100 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain C residue 13 HIS Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 11 GLU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain E residue 10 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain F residue 28 LYS Chi-restraints excluded: chain F residue 35 MET Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain J residue 28 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 HIS H 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.109603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.096211 restraints weight = 5915.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.098201 restraints weight = 2616.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.099425 restraints weight = 1654.492| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.7845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3000 Z= 0.185 Angle : 0.621 6.950 4020 Z= 0.320 Chirality : 0.050 0.152 425 Planarity : 0.002 0.016 525 Dihedral : 7.398 48.764 415 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 6.00 % Allowed : 31.00 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.82 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 14 PHE 0.010 0.001 PHE D 20 TYR 0.006 0.001 TYR G 10 ARG 0.001 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1072.22 seconds wall clock time: 20 minutes 21.30 seconds (1221.30 seconds total)