Starting phenix.real_space_refine on Sun Mar 10 15:18:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oln_16959/03_2024/8oln_16959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oln_16959/03_2024/8oln_16959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oln_16959/03_2024/8oln_16959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oln_16959/03_2024/8oln_16959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oln_16959/03_2024/8oln_16959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oln_16959/03_2024/8oln_16959.pdb" } resolution = 3.3 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= 0.000 sd= 1.001 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 1800 2.51 5 N 510 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2830 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "J" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "B" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "D" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "E" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "F" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "H" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "I" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Time building chain proxies: 1.96, per 1000 atoms: 0.69 Number of scatterers: 2830 At special positions: 0 Unit cell: (91.304, 89.688, 42.016, 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 510 8.00 N 510 7.00 C 1800 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 - 3.50 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: 1.00 Conformation dependent library (CDL) restraints added in 500.6 milliseconds 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 640 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.510A pdb=" N ALA A 2 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ARG C 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 4 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASP C 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.510A pdb=" N ALA A 2 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ARG C 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 4 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASP C 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 2 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG E 5 " --> pdb=" O ALA C 2 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N PHE C 4 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP E 7 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N HIS C 6 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLY E 9 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER C 8 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLU E 11 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR C 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N HIS E 13 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA E 2 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ARG G 5 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE E 4 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP G 7 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS E 6 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY G 9 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER E 8 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLU G 11 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N HIS G 13 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU I 3 " --> pdb=" O ALA G 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS G 6 " --> pdb=" O ARG I 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 24 removed outlier: 6.783A pdb=" N ALA A 21 " --> pdb=" O GLN C 22 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL C 24 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN A 23 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 21 " --> pdb=" O GLN E 22 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL E 24 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN C 23 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA E 21 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL G 24 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN E 23 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA G 21 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL I 24 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN G 23 " --> pdb=" O VAL I 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA5, first strand: chain 'J' and resid 2 through 13 removed outlier: 6.711A pdb=" N GLU J 3 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N HIS H 6 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ARG J 5 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N SER H 8 " --> pdb=" O ARG J 5 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP J 7 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR H 10 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY J 9 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL H 12 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU J 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA F 2 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG H 5 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE F 4 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP H 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS F 6 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLY H 9 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER F 8 " --> pdb=" O GLY H 9 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLU H 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR F 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N HIS H 13 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 12 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA D 2 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG F 5 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE D 4 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP F 7 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS D 6 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY F 9 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER D 8 " --> pdb=" O GLY F 9 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU F 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR D 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N HIS F 13 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL D 12 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 2 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ARG D 5 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE B 4 " --> pdb=" O ARG D 5 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP D 7 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS B 6 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY D 9 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER B 8 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU D 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N HIS D 13 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'J' and resid 21 through 24 removed outlier: 6.810A pdb=" N ALA F 21 " --> pdb=" O GLN H 22 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL H 24 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN F 23 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA D 21 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL F 24 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN D 23 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA B 21 " --> pdb=" O GLN D 22 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 24 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN B 23 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 30 through 32 removed outlier: 6.179A pdb=" N ILE J 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.503A pdb=" N VAL C 18 " --> pdb=" O LEU E 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 17 through 18 36 hydrogen bonds defined for protein. 108 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: 0.60 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 960 1.34 - 1.46: 655 1.46 - 1.57: 1255 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2890 Sorted by residual: bond pdb=" CA VAL J 12 " pdb=" CB VAL J 12 " ideal model delta sigma weight residual 1.548 1.539 0.009 1.13e-02 7.83e+03 5.93e-01 bond pdb=" CA VAL I 12 " pdb=" CB VAL I 12 " ideal model delta sigma weight residual 1.548 1.539 0.008 1.13e-02 7.83e+03 5.38e-01 bond pdb=" CA VAL G 18 " pdb=" CB VAL G 18 " ideal model delta sigma weight residual 1.548 1.539 0.008 1.13e-02 7.83e+03 5.36e-01 bond pdb=" CA VAL C 18 " pdb=" CB VAL C 18 " ideal model delta sigma weight residual 1.548 1.539 0.008 1.13e-02 7.83e+03 5.31e-01 bond pdb=" CA VAL F 12 " pdb=" CB VAL F 12 " ideal model delta sigma weight residual 1.548 1.540 0.008 1.13e-02 7.83e+03 5.00e-01 ... (remaining 2885 not shown) Histogram of bond angle deviations from ideal: 100.86 - 106.94: 40 106.94 - 113.02: 1550 113.02 - 119.10: 700 119.10 - 125.18: 1550 125.18 - 131.26: 30 Bond angle restraints: 3870 Sorted by residual: angle pdb=" N ALA B 2 " pdb=" CA ALA B 2 " pdb=" C ALA B 2 " ideal model delta sigma weight residual 108.32 111.26 -2.94 1.64e+00 3.72e-01 3.20e+00 angle pdb=" N ALA F 2 " pdb=" CA ALA F 2 " pdb=" C ALA F 2 " ideal model delta sigma weight residual 108.32 111.24 -2.92 1.64e+00 3.72e-01 3.18e+00 angle pdb=" N ALA D 2 " pdb=" CA ALA D 2 " pdb=" C ALA D 2 " ideal model delta sigma weight residual 108.32 111.24 -2.92 1.64e+00 3.72e-01 3.17e+00 angle pdb=" N ALA J 2 " pdb=" CA ALA J 2 " pdb=" C ALA J 2 " ideal model delta sigma weight residual 108.32 111.23 -2.91 1.64e+00 3.72e-01 3.14e+00 angle pdb=" N ALA G 2 " pdb=" CA ALA G 2 " pdb=" C ALA G 2 " ideal model delta sigma weight residual 108.32 111.22 -2.90 1.64e+00 3.72e-01 3.14e+00 ... (remaining 3865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.02: 1270 6.02 - 12.05: 220 12.05 - 18.07: 80 18.07 - 24.09: 30 24.09 - 30.12: 40 Dihedral angle restraints: 1640 sinusoidal: 640 harmonic: 1000 Sorted by residual: dihedral pdb=" CA LYS B 28 " pdb=" CB LYS B 28 " pdb=" CG LYS B 28 " pdb=" CD LYS B 28 " ideal model delta sinusoidal sigma weight residual -180.00 -149.88 -30.12 3 1.50e+01 4.44e-03 4.77e+00 dihedral pdb=" CA LYS E 28 " pdb=" CB LYS E 28 " pdb=" CG LYS E 28 " pdb=" CD LYS E 28 " ideal model delta sinusoidal sigma weight residual -180.00 -149.91 -30.09 3 1.50e+01 4.44e-03 4.76e+00 dihedral pdb=" CA LYS I 28 " pdb=" CB LYS I 28 " pdb=" CG LYS I 28 " pdb=" CD LYS I 28 " ideal model delta sinusoidal sigma weight residual -180.00 -149.93 -30.07 3 1.50e+01 4.44e-03 4.76e+00 ... (remaining 1637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 187 0.025 - 0.049: 143 0.049 - 0.074: 20 0.074 - 0.099: 27 0.099 - 0.123: 23 Chirality restraints: 400 Sorted by residual: chirality pdb=" CA ILE I 31 " pdb=" N ILE I 31 " pdb=" C ILE I 31 " pdb=" CB ILE I 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 397 not shown) Planarity restraints: 510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 5 " -0.002 2.00e-02 2.50e+03 3.88e-03 1.51e-01 pdb=" C ARG E 5 " 0.007 2.00e-02 2.50e+03 pdb=" O ARG E 5 " -0.003 2.00e-02 2.50e+03 pdb=" N HIS E 6 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 5 " -0.002 2.00e-02 2.50e+03 3.88e-03 1.50e-01 pdb=" C ARG H 5 " 0.007 2.00e-02 2.50e+03 pdb=" O ARG H 5 " -0.003 2.00e-02 2.50e+03 pdb=" N HIS H 6 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG J 5 " -0.002 2.00e-02 2.50e+03 3.68e-03 1.36e-01 pdb=" C ARG J 5 " 0.006 2.00e-02 2.50e+03 pdb=" O ARG J 5 " -0.002 2.00e-02 2.50e+03 pdb=" N HIS J 6 " -0.002 2.00e-02 2.50e+03 ... (remaining 507 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 611 2.80 - 3.32: 2443 3.32 - 3.85: 4757 3.85 - 4.37: 5160 4.37 - 4.90: 9774 Nonbonded interactions: 22745 Sorted by model distance: nonbonded pdb=" OD1 ASP F 1 " pdb=" N ASP H 1 " model vdw 2.271 2.520 nonbonded pdb=" OD1 ASP C 1 " pdb=" N ASP E 1 " model vdw 2.305 2.520 nonbonded pdb=" O ASN D 23 " pdb=" OH TYR F 10 " model vdw 2.430 2.440 nonbonded pdb=" OD1 ASP B 1 " pdb=" N ASP D 1 " model vdw 2.439 2.520 nonbonded pdb=" O ASN G 23 " pdb=" OH TYR I 10 " model vdw 2.455 2.440 ... (remaining 22740 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.000 Extract box with map and model: 5.530 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.590 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.002 0.009 2890 Z= 0.148 Angle : 0.479 2.936 3870 Z= 0.307 Chirality : 0.044 0.123 400 Planarity : 0.001 0.005 510 Dihedral : 9.035 30.117 1000 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.41 % Allowed : 4.48 % Favored : 93.10 % 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: -4.24 (0.32), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 13 PHE 0.003 0.001 PHE G 4 TYR 0.004 0.001 TYR A 10 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 0.326 Fit side-chains REVERT: A 5 ARG cc_start: 0.5642 (ptm-80) cc_final: 0.5275 (ptt90) REVERT: J 5 ARG cc_start: 0.7146 (ptm-80) cc_final: 0.5757 (mmm160) REVERT: J 10 TYR cc_start: 0.8407 (t80) cc_final: 0.5764 (p90) REVERT: J 19 PHE cc_start: 0.8262 (t80) cc_final: 0.7953 (t80) REVERT: B 5 ARG cc_start: 0.6090 (ptm-80) cc_final: 0.5215 (ptt-90) REVERT: B 19 PHE cc_start: 0.8523 (t80) cc_final: 0.8154 (t80) REVERT: B 22 GLN cc_start: 0.8531 (mt0) cc_final: 0.7526 (pm20) REVERT: C 19 PHE cc_start: 0.8513 (t80) cc_final: 0.7923 (t80) REVERT: D 19 PHE cc_start: 0.8452 (t80) cc_final: 0.7837 (t80) REVERT: E 19 PHE cc_start: 0.8587 (t80) cc_final: 0.8037 (t80) REVERT: F 19 PHE cc_start: 0.8532 (t80) cc_final: 0.8058 (t80) REVERT: G 19 PHE cc_start: 0.8557 (t80) cc_final: 0.8183 (t80) REVERT: H 5 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7143 (ttp-110) REVERT: H 19 PHE cc_start: 0.8602 (t80) cc_final: 0.8302 (t80) REVERT: I 10 TYR cc_start: 0.8295 (t80) cc_final: 0.5903 (p90) REVERT: I 19 PHE cc_start: 0.8176 (t80) cc_final: 0.7527 (t80) REVERT: I 23 ASN cc_start: 0.8235 (m-40) cc_final: 0.7873 (m-40) outliers start: 7 outliers final: 5 residues processed: 183 average time/residue: 0.1791 time to fit residues: 37.4274 Evaluate side-chains 139 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 0.0670 chunk 15 optimal weight: 0.0070 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.0060 chunk 8 optimal weight: 2.9990 overall best weight: 1.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS J 13 HIS J 14 HIS J 22 GLN B 14 HIS C 14 HIS ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 HIS D 22 GLN E 14 HIS E 15 GLN E 22 GLN F 14 HIS F 22 GLN G 14 HIS G 15 GLN H 14 HIS H 22 GLN I 13 HIS I 14 HIS I 22 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2890 Z= 0.157 Angle : 0.437 4.916 3870 Z= 0.249 Chirality : 0.050 0.138 400 Planarity : 0.002 0.020 510 Dihedral : 4.383 15.932 375 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.90 % Allowed : 14.48 % Favored : 78.62 % 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: -4.31 (0.34), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.26), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 13 PHE 0.012 0.001 PHE D 4 TYR 0.011 0.001 TYR G 10 ARG 0.005 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 0.323 Fit side-chains REVERT: A 32 ILE cc_start: 0.7882 (mm) cc_final: 0.7560 (mm) REVERT: J 10 TYR cc_start: 0.8329 (t80) cc_final: 0.5897 (p90) REVERT: J 19 PHE cc_start: 0.8481 (t80) cc_final: 0.7709 (t80) REVERT: B 19 PHE cc_start: 0.8329 (t80) cc_final: 0.8088 (t80) REVERT: B 32 ILE cc_start: 0.7689 (mm) cc_final: 0.7394 (mm) REVERT: B 36 VAL cc_start: 0.8030 (m) cc_final: 0.7811 (t) REVERT: C 19 PHE cc_start: 0.8529 (t80) cc_final: 0.7905 (t80) REVERT: D 19 PHE cc_start: 0.8360 (t80) cc_final: 0.7905 (t80) REVERT: E 19 PHE cc_start: 0.8644 (t80) cc_final: 0.8111 (t80) REVERT: F 19 PHE cc_start: 0.8536 (t80) cc_final: 0.8052 (t80) REVERT: H 10 TYR cc_start: 0.9103 (t80) cc_final: 0.8477 (t80) REVERT: I 10 TYR cc_start: 0.8324 (t80) cc_final: 0.6062 (p90) REVERT: I 16 LYS cc_start: 0.4889 (mmtt) cc_final: 0.3932 (mttt) REVERT: I 22 GLN cc_start: 0.8924 (mt0) cc_final: 0.8628 (mt0) outliers start: 20 outliers final: 16 residues processed: 152 average time/residue: 0.1560 time to fit residues: 27.5742 Evaluate side-chains 138 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS B 13 HIS C 13 HIS ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 HIS E 22 GLN F 13 HIS G 13 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 HIS H 22 GLN ** H 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.009 0.042 2890 Z= 0.594 Angle : 0.661 6.030 3870 Z= 0.379 Chirality : 0.052 0.148 400 Planarity : 0.003 0.024 510 Dihedral : 5.310 28.245 372 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 10.34 % Allowed : 19.31 % Favored : 70.34 % 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: -4.58 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 13 PHE 0.017 0.002 PHE E 4 TYR 0.008 0.002 TYR G 10 ARG 0.002 0.001 ARG J 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 0.480 Fit side-chains REVERT: A 19 PHE cc_start: 0.8523 (t80) cc_final: 0.8259 (t80) REVERT: A 28 LYS cc_start: 0.9395 (mtpp) cc_final: 0.9182 (mtpp) REVERT: A 32 ILE cc_start: 0.8623 (mm) cc_final: 0.8399 (mm) REVERT: J 7 ASP cc_start: 0.7475 (t0) cc_final: 0.7185 (t70) REVERT: D 19 PHE cc_start: 0.8287 (t80) cc_final: 0.7840 (t80) REVERT: F 19 PHE cc_start: 0.8600 (t80) cc_final: 0.8146 (t80) REVERT: H 17 LEU cc_start: 0.8814 (mp) cc_final: 0.8507 (mp) REVERT: I 7 ASP cc_start: 0.7455 (t0) cc_final: 0.7209 (t70) REVERT: I 22 GLN cc_start: 0.8940 (mt0) cc_final: 0.8710 (mt0) outliers start: 30 outliers final: 23 residues processed: 141 average time/residue: 0.1513 time to fit residues: 25.6648 Evaluate side-chains 137 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2890 Z= 0.230 Angle : 0.464 5.149 3870 Z= 0.264 Chirality : 0.050 0.142 400 Planarity : 0.002 0.009 510 Dihedral : 4.673 18.355 372 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 10.00 % Allowed : 22.41 % Favored : 67.59 % 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: -4.55 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 13 PHE 0.008 0.001 PHE E 4 TYR 0.009 0.001 TYR H 10 ARG 0.002 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 0.342 Fit side-chains REVERT: A 19 PHE cc_start: 0.8578 (t80) cc_final: 0.8241 (t80) REVERT: A 32 ILE cc_start: 0.8349 (mm) cc_final: 0.8090 (mm) REVERT: J 7 ASP cc_start: 0.7381 (t0) cc_final: 0.7151 (t70) REVERT: J 19 PHE cc_start: 0.8675 (t80) cc_final: 0.8369 (t80) REVERT: C 19 PHE cc_start: 0.8544 (t80) cc_final: 0.8130 (t80) REVERT: D 19 PHE cc_start: 0.8204 (t80) cc_final: 0.7649 (t80) REVERT: F 19 PHE cc_start: 0.8691 (t80) cc_final: 0.8265 (t80) REVERT: I 22 GLN cc_start: 0.8880 (mt0) cc_final: 0.8597 (mt0) outliers start: 29 outliers final: 24 residues processed: 146 average time/residue: 0.1432 time to fit residues: 24.7422 Evaluate side-chains 140 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain H residue 8 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 0.0670 chunk 0 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 0.0470 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN E 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2890 Z= 0.237 Angle : 0.466 4.661 3870 Z= 0.267 Chirality : 0.049 0.140 400 Planarity : 0.002 0.025 510 Dihedral : 4.821 19.140 372 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 10.34 % Allowed : 21.72 % Favored : 67.93 % 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: -4.53 (0.34), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.26), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.012 0.001 PHE G 19 TYR 0.008 0.001 TYR H 10 ARG 0.001 0.000 ARG H 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 0.332 Fit side-chains REVERT: A 19 PHE cc_start: 0.8610 (t80) cc_final: 0.8261 (t80) REVERT: A 32 ILE cc_start: 0.8335 (mm) cc_final: 0.8118 (mm) REVERT: J 7 ASP cc_start: 0.7292 (t0) cc_final: 0.7040 (t70) REVERT: J 19 PHE cc_start: 0.8684 (t80) cc_final: 0.8378 (t80) REVERT: C 19 PHE cc_start: 0.8572 (t80) cc_final: 0.8140 (t80) REVERT: D 19 PHE cc_start: 0.8156 (t80) cc_final: 0.7679 (t80) REVERT: F 19 PHE cc_start: 0.8688 (t80) cc_final: 0.8295 (t80) REVERT: G 19 PHE cc_start: 0.8566 (t80) cc_final: 0.8232 (t80) REVERT: I 19 PHE cc_start: 0.8694 (t80) cc_final: 0.8359 (t80) REVERT: I 22 GLN cc_start: 0.8898 (mt0) cc_final: 0.8626 (mt0) outliers start: 30 outliers final: 27 residues processed: 138 average time/residue: 0.1379 time to fit residues: 22.6462 Evaluate side-chains 139 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 2890 Z= 0.498 Angle : 0.603 5.295 3870 Z= 0.345 Chirality : 0.050 0.139 400 Planarity : 0.003 0.019 510 Dihedral : 5.334 24.618 372 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 11.72 % Allowed : 21.03 % Favored : 67.24 % 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: -4.56 (0.34), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.26), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 13 PHE 0.016 0.002 PHE H 4 TYR 0.014 0.002 TYR I 10 ARG 0.002 0.000 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 0.328 Fit side-chains REVERT: A 19 PHE cc_start: 0.8517 (t80) cc_final: 0.8209 (t80) REVERT: J 7 ASP cc_start: 0.7130 (t0) cc_final: 0.6816 (t70) REVERT: J 19 PHE cc_start: 0.8674 (t80) cc_final: 0.8354 (t80) REVERT: C 19 PHE cc_start: 0.8586 (t80) cc_final: 0.8179 (t80) REVERT: F 19 PHE cc_start: 0.8665 (t80) cc_final: 0.8276 (t80) REVERT: G 19 PHE cc_start: 0.8555 (t80) cc_final: 0.8309 (t80) REVERT: I 7 ASP cc_start: 0.7167 (t0) cc_final: 0.6921 (t70) REVERT: I 22 GLN cc_start: 0.8934 (mt0) cc_final: 0.8638 (mt0) outliers start: 34 outliers final: 30 residues processed: 145 average time/residue: 0.1488 time to fit residues: 25.4405 Evaluate side-chains 150 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN C 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2890 Z= 0.322 Angle : 0.507 5.689 3870 Z= 0.291 Chirality : 0.050 0.144 400 Planarity : 0.002 0.015 510 Dihedral : 5.050 20.803 372 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 11.38 % Allowed : 22.07 % Favored : 66.55 % 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: -4.50 (0.35), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.26), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 13 PHE 0.009 0.001 PHE E 4 TYR 0.014 0.002 TYR H 10 ARG 0.001 0.000 ARG J 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 0.314 Fit side-chains REVERT: A 19 PHE cc_start: 0.8622 (t80) cc_final: 0.8311 (t80) REVERT: J 7 ASP cc_start: 0.7085 (t0) cc_final: 0.6764 (t70) REVERT: J 19 PHE cc_start: 0.8673 (t80) cc_final: 0.8384 (t80) REVERT: C 19 PHE cc_start: 0.8605 (t80) cc_final: 0.8221 (t80) REVERT: D 19 PHE cc_start: 0.8205 (t80) cc_final: 0.7774 (t80) REVERT: F 19 PHE cc_start: 0.8675 (t80) cc_final: 0.8312 (t80) REVERT: G 19 PHE cc_start: 0.8490 (t80) cc_final: 0.8159 (t80) REVERT: I 7 ASP cc_start: 0.7129 (t0) cc_final: 0.6633 (t70) REVERT: I 19 PHE cc_start: 0.8632 (t80) cc_final: 0.8217 (t80) REVERT: I 20 PHE cc_start: 0.8684 (m-10) cc_final: 0.8218 (m-80) REVERT: I 22 GLN cc_start: 0.8881 (mt0) cc_final: 0.8572 (mt0) outliers start: 33 outliers final: 31 residues processed: 140 average time/residue: 0.1364 time to fit residues: 22.6803 Evaluate side-chains 149 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0370 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2890 Z= 0.266 Angle : 0.474 5.733 3870 Z= 0.272 Chirality : 0.050 0.143 400 Planarity : 0.002 0.014 510 Dihedral : 4.895 19.663 372 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 11.72 % Allowed : 22.07 % Favored : 66.21 % 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: -4.50 (0.35), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.27), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.009 0.001 PHE F 4 TYR 0.016 0.002 TYR H 10 ARG 0.001 0.000 ARG J 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 117 time to evaluate : 0.339 Fit side-chains REVERT: A 19 PHE cc_start: 0.8663 (t80) cc_final: 0.8345 (t80) REVERT: A 36 VAL cc_start: 0.8103 (m) cc_final: 0.7896 (t) REVERT: J 7 ASP cc_start: 0.7061 (t0) cc_final: 0.6745 (t70) REVERT: J 19 PHE cc_start: 0.8694 (t80) cc_final: 0.8420 (t80) REVERT: C 19 PHE cc_start: 0.8690 (t80) cc_final: 0.8113 (t80) REVERT: D 19 PHE cc_start: 0.8136 (t80) cc_final: 0.7723 (t80) REVERT: E 19 PHE cc_start: 0.8477 (t80) cc_final: 0.8058 (t80) REVERT: E 20 PHE cc_start: 0.8892 (m-80) cc_final: 0.8686 (m-10) REVERT: F 19 PHE cc_start: 0.8683 (t80) cc_final: 0.8336 (t80) REVERT: G 19 PHE cc_start: 0.8485 (t80) cc_final: 0.8167 (t80) REVERT: I 7 ASP cc_start: 0.7059 (t0) cc_final: 0.6557 (t70) REVERT: I 19 PHE cc_start: 0.8661 (t80) cc_final: 0.8216 (t80) REVERT: I 20 PHE cc_start: 0.8735 (m-10) cc_final: 0.8208 (m-80) REVERT: I 22 GLN cc_start: 0.8886 (mt0) cc_final: 0.8581 (mt0) outliers start: 34 outliers final: 32 residues processed: 139 average time/residue: 0.1309 time to fit residues: 21.8445 Evaluate side-chains 147 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2890 Z= 0.207 Angle : 0.449 5.907 3870 Z= 0.256 Chirality : 0.049 0.142 400 Planarity : 0.002 0.012 510 Dihedral : 4.743 18.520 372 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 11.03 % Allowed : 22.76 % Favored : 66.21 % 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: -4.44 (0.35), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.27), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.008 0.001 PHE C 19 TYR 0.015 0.002 TYR H 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 0.334 Fit side-chains REVERT: A 19 PHE cc_start: 0.8744 (t80) cc_final: 0.8484 (t80) REVERT: J 7 ASP cc_start: 0.7102 (t0) cc_final: 0.6753 (t70) REVERT: J 19 PHE cc_start: 0.8692 (t80) cc_final: 0.8456 (t80) REVERT: C 19 PHE cc_start: 0.8601 (t80) cc_final: 0.8263 (t80) REVERT: D 19 PHE cc_start: 0.8047 (t80) cc_final: 0.7659 (t80) REVERT: F 19 PHE cc_start: 0.8684 (t80) cc_final: 0.8348 (t80) REVERT: G 19 PHE cc_start: 0.8507 (t80) cc_final: 0.8215 (t80) REVERT: I 7 ASP cc_start: 0.7135 (t0) cc_final: 0.6872 (t70) REVERT: I 19 PHE cc_start: 0.8694 (t80) cc_final: 0.8256 (t80) REVERT: I 20 PHE cc_start: 0.8699 (m-10) cc_final: 0.8151 (m-80) REVERT: I 22 GLN cc_start: 0.8904 (mt0) cc_final: 0.8605 (mt0) outliers start: 32 outliers final: 30 residues processed: 143 average time/residue: 0.1307 time to fit residues: 22.4562 Evaluate side-chains 150 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.0870 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 1 optimal weight: 0.0980 chunk 17 optimal weight: 9.9990 overall best weight: 6.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 2890 Z= 0.469 Angle : 0.591 5.729 3870 Z= 0.339 Chirality : 0.051 0.142 400 Planarity : 0.003 0.017 510 Dihedral : 5.342 23.967 372 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 11.38 % Allowed : 23.10 % Favored : 65.52 % 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: -4.49 (0.35), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.27), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 13 PHE 0.013 0.002 PHE H 4 TYR 0.019 0.003 TYR F 10 ARG 0.002 0.001 ARG B 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 0.349 Fit side-chains REVERT: A 19 PHE cc_start: 0.8667 (t80) cc_final: 0.8391 (t80) REVERT: J 7 ASP cc_start: 0.7200 (t0) cc_final: 0.6834 (t70) REVERT: J 19 PHE cc_start: 0.8680 (t80) cc_final: 0.8383 (t80) REVERT: C 19 PHE cc_start: 0.8389 (t80) cc_final: 0.8054 (t80) REVERT: D 19 PHE cc_start: 0.8239 (t80) cc_final: 0.7858 (t80) REVERT: F 19 PHE cc_start: 0.8683 (t80) cc_final: 0.8310 (t80) REVERT: G 19 PHE cc_start: 0.8550 (t80) cc_final: 0.8294 (t80) REVERT: I 7 ASP cc_start: 0.6994 (t0) cc_final: 0.6688 (t70) REVERT: I 19 PHE cc_start: 0.8698 (t80) cc_final: 0.8348 (t80) REVERT: I 22 GLN cc_start: 0.8914 (mt0) cc_final: 0.8627 (mt0) outliers start: 33 outliers final: 31 residues processed: 141 average time/residue: 0.1465 time to fit residues: 24.7270 Evaluate side-chains 147 residues out of total 290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 8 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** 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 = 0.4315 r_free = 0.4315 target = 0.159750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.141286 restraints weight = 4968.783| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 4.59 r_work: 0.3917 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2890 Z= 0.411 Angle : 0.561 5.854 3870 Z= 0.321 Chirality : 0.051 0.148 400 Planarity : 0.003 0.015 510 Dihedral : 5.302 20.809 372 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 10.69 % Allowed : 23.79 % Favored : 65.52 % 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: -4.45 (0.36), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.27), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 13 PHE 0.014 0.002 PHE B 20 TYR 0.020 0.003 TYR E 10 ARG 0.001 0.000 ARG B 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1191.95 seconds wall clock time: 22 minutes 8.73 seconds (1328.73 seconds total)