Starting phenix.real_space_refine on Thu Dec 7 16:46:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/12_2023/8bfa_16018.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/12_2023/8bfa_16018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/12_2023/8bfa_16018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/12_2023/8bfa_16018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/12_2023/8bfa_16018.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bfa_16018/12_2023/8bfa_16018.pdb" } resolution = 3.0 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1810 2.51 5 N 510 2.21 5 O 530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2860 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "B" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "C" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "D" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "F" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "G" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "H" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "I" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "J" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 286 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Time building chain proxies: 1.91, per 1000 atoms: 0.67 Number of scatterers: 2860 At special positions: 0 Unit cell: (90.47, 67.23, 39.84, 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 530 8.00 N 510 7.00 C 1810 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: 0.93 Conformation dependent library (CDL) restraints added in 508.2 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 620 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 52.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 6.163A pdb=" N PHE E 4 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP G 7 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS E 6 " --> pdb=" O ASP G 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.385A pdb=" N GLU A 11 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS C 14 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N HIS A 13 " --> pdb=" O HIS C 14 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LYS C 16 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN A 15 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU E 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS G 14 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS E 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LYS G 16 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN E 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS I 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N HIS G 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LYS I 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN G 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.818A pdb=" N SER C 26 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN A 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER E 26 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASN C 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER G 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 27 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER I 26 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN G 27 " --> pdb=" O SER I 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.398A pdb=" N ALA A 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY C 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N ILE A 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET C 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU A 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA C 30 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLY E 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ILE C 32 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N MET E 35 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LEU C 34 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA E 30 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLY G 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N ILE E 32 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET G 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LEU E 34 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA G 30 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLY I 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ILE G 32 " --> pdb=" O GLY I 33 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET I 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N LEU G 34 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 7 removed outlier: 6.150A pdb=" N PHE D 4 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASP F 7 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS D 6 " --> pdb=" O ASP F 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 16 removed outlier: 6.393A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HIS D 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N HIS B 13 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS D 16 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N HIS F 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS D 13 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LYS F 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N HIS H 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS F 13 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LYS H 16 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN F 15 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU H 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS J 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N HIS H 13 " --> pdb=" O HIS J 14 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LYS J 16 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN H 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 21 Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.835A pdb=" N SER D 26 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN B 27 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER F 26 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASN D 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER H 26 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASN F 27 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER J 26 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN H 27 " --> pdb=" O SER J 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.406A pdb=" N ALA B 30 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY D 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N ILE B 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET D 35 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N LEU B 34 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA D 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY F 33 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ILE D 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N MET F 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LEU D 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA F 30 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLY H 33 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE F 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET H 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N LEU F 34 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA H 30 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY J 33 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N ILE H 32 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N MET J 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N LEU H 34 " --> pdb=" O MET J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 46 hydrogen bonds defined for protein. 138 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: 0.69 Time building geometry restraints manager: 1.03 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: 980 1.34 - 1.46: 648 1.46 - 1.57: 1272 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2920 Sorted by residual: bond pdb=" N ARG J 5 " pdb=" CA ARG J 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.65e+00 bond pdb=" N ARG B 5 " pdb=" CA ARG B 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.55e+00 bond pdb=" N ARG I 5 " pdb=" CA ARG I 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.54e+00 bond pdb=" N ARG E 5 " pdb=" CA ARG E 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.45e+00 bond pdb=" N ARG C 5 " pdb=" CA ARG C 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.43e+00 ... (remaining 2915 not shown) Histogram of bond angle deviations from ideal: 101.10 - 107.14: 51 107.14 - 113.18: 1490 113.18 - 119.21: 779 119.21 - 125.25: 1550 125.25 - 131.29: 30 Bond angle restraints: 3900 Sorted by residual: angle pdb=" CA ARG A 5 " pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 120.24 118.31 1.93 1.06e+00 8.90e-01 3.33e+00 angle pdb=" CA ARG B 5 " pdb=" C ARG B 5 " pdb=" O ARG B 5 " ideal model delta sigma weight residual 120.24 118.32 1.92 1.06e+00 8.90e-01 3.27e+00 angle pdb=" CA ARG G 5 " pdb=" C ARG G 5 " pdb=" O ARG G 5 " ideal model delta sigma weight residual 120.24 118.34 1.90 1.06e+00 8.90e-01 3.22e+00 angle pdb=" CA ARG F 5 " pdb=" C ARG F 5 " pdb=" O ARG F 5 " ideal model delta sigma weight residual 120.24 118.34 1.90 1.06e+00 8.90e-01 3.21e+00 angle pdb=" CA ARG I 5 " pdb=" C ARG I 5 " pdb=" O ARG I 5 " ideal model delta sigma weight residual 120.24 118.35 1.89 1.06e+00 8.90e-01 3.19e+00 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1440 13.04 - 26.08: 90 26.08 - 39.13: 40 39.13 - 52.17: 30 52.17 - 65.21: 10 Dihedral angle restraints: 1610 sinusoidal: 610 harmonic: 1000 Sorted by residual: dihedral pdb=" CA LEU E 34 " pdb=" CB LEU E 34 " pdb=" CG LEU E 34 " pdb=" CD1 LEU E 34 " ideal model delta sinusoidal sigma weight residual 180.00 139.97 40.03 3 1.50e+01 4.44e-03 7.12e+00 dihedral pdb=" CA LEU I 34 " pdb=" CB LEU I 34 " pdb=" CG LEU I 34 " pdb=" CD1 LEU I 34 " ideal model delta sinusoidal sigma weight residual 180.00 140.02 39.98 3 1.50e+01 4.44e-03 7.11e+00 dihedral pdb=" CA LEU H 34 " pdb=" CB LEU H 34 " pdb=" CG LEU H 34 " pdb=" CD1 LEU H 34 " ideal model delta sinusoidal sigma weight residual 180.00 140.03 39.97 3 1.50e+01 4.44e-03 7.10e+00 ... (remaining 1607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 149 0.024 - 0.049: 133 0.049 - 0.073: 48 0.073 - 0.098: 3 0.098 - 0.122: 57 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ARG H 5 " pdb=" N ARG H 5 " pdb=" C ARG H 5 " pdb=" CB ARG H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ARG E 5 " pdb=" N ARG E 5 " pdb=" C ARG E 5 " pdb=" CB ARG E 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ARG F 5 " pdb=" N ARG F 5 " pdb=" C ARG F 5 " pdb=" CB ARG F 5 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 387 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.003 2.00e-02 2.50e+03 2.70e-03 1.28e-01 pdb=" CG PHE A 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 4 " -0.002 2.00e-02 2.50e+03 2.51e-03 1.11e-01 pdb=" CG PHE G 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE G 4 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE G 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 4 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE G 4 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 4 " -0.002 2.00e-02 2.50e+03 2.50e-03 1.10e-01 pdb=" CG PHE C 4 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE C 4 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 4 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 4 " -0.000 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1663 3.05 - 3.51: 2612 3.51 - 3.98: 4531 3.98 - 4.44: 4981 4.44 - 4.90: 10405 Nonbonded interactions: 24192 Sorted by model distance: nonbonded pdb=" NZ LYS G 28 " pdb=" OE2 GLU H 11 " model vdw 2.592 2.520 nonbonded pdb=" NZ LYS E 28 " pdb=" OE2 GLU F 11 " model vdw 2.603 2.520 nonbonded pdb=" NZ LYS F 28 " pdb=" OE2 GLU G 11 " model vdw 2.609 2.520 nonbonded pdb=" NZ LYS I 28 " pdb=" OE2 GLU J 11 " model vdw 2.618 2.520 nonbonded pdb=" NZ LYS H 28 " pdb=" OE2 GLU I 11 " model vdw 2.618 2.520 ... (remaining 24187 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: 1.090 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: 5.400 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.290 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 0.028 2920 Z= 0.171 Angle : 0.386 2.691 3900 Z= 0.246 Chirality : 0.052 0.122 390 Planarity : 0.001 0.003 520 Dihedral : 13.944 65.212 990 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -3.13 (0.34), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 6 PHE 0.006 0.001 PHE A 4 TYR 0.004 0.001 TYR C 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 1.3103 time to fit residues: 67.1380 Evaluate side-chains 31 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 13 HIS B 27 ASN C 27 ASN D 27 ASN E 13 HIS E 27 ASN F 27 ASN G 27 ASN H 27 ASN I 27 ASN J 27 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 2920 Z= 0.566 Angle : 0.582 4.602 3900 Z= 0.324 Chirality : 0.053 0.136 390 Planarity : 0.004 0.026 520 Dihedral : 5.212 14.287 390 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 8.21 % Allowed : 10.71 % Favored : 81.07 % 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: -2.81 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 13 PHE 0.014 0.003 PHE F 4 TYR 0.012 0.003 TYR C 10 ARG 0.001 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 39 time to evaluate : 0.325 Fit side-chains outliers start: 23 outliers final: 9 residues processed: 60 average time/residue: 1.3367 time to fit residues: 82.0849 Evaluate side-chains 45 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 0.1762 time to fit residues: 0.5777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2920 Z= 0.290 Angle : 0.493 4.099 3900 Z= 0.263 Chirality : 0.052 0.131 390 Planarity : 0.002 0.009 520 Dihedral : 4.448 11.444 390 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 6.07 % Allowed : 13.93 % Favored : 80.00 % 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: -2.71 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.011 0.002 PHE I 4 TYR 0.005 0.001 TYR C 10 ARG 0.002 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 36 time to evaluate : 0.346 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 47 average time/residue: 1.4470 time to fit residues: 69.6129 Evaluate side-chains 40 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 2920 Z= 0.480 Angle : 0.559 4.275 3900 Z= 0.300 Chirality : 0.053 0.132 390 Planarity : 0.002 0.017 520 Dihedral : 5.175 14.360 390 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 6.43 % Allowed : 15.36 % Favored : 78.21 % 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: -2.71 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 13 PHE 0.014 0.002 PHE D 4 TYR 0.007 0.002 TYR C 10 ARG 0.002 0.001 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 36 time to evaluate : 0.321 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 53 average time/residue: 1.4765 time to fit residues: 80.0053 Evaluate side-chains 42 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.316 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 0.1633 time to fit residues: 0.5992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 HIS G 13 HIS H 13 HIS J 13 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2920 Z= 0.175 Angle : 0.444 3.840 3900 Z= 0.241 Chirality : 0.051 0.131 390 Planarity : 0.001 0.015 520 Dihedral : 4.219 11.490 390 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 5.36 % Allowed : 17.86 % Favored : 76.79 % 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: -2.66 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 13 PHE 0.008 0.001 PHE D 4 TYR 0.003 0.001 TYR C 10 ARG 0.003 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 34 time to evaluate : 0.319 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 46 average time/residue: 1.5187 time to fit residues: 71.3703 Evaluate side-chains 35 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.306 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 0.0050 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2920 Z= 0.379 Angle : 0.538 4.641 3900 Z= 0.285 Chirality : 0.052 0.131 390 Planarity : 0.002 0.011 520 Dihedral : 4.774 12.756 390 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.21 % Allowed : 21.07 % Favored : 75.71 % 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: -2.68 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 13 PHE 0.012 0.002 PHE D 4 TYR 0.006 0.002 TYR I 10 ARG 0.002 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.294 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 1.4639 time to fit residues: 62.9681 Evaluate side-chains 35 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2920 Z= 0.214 Angle : 0.458 4.218 3900 Z= 0.245 Chirality : 0.052 0.132 390 Planarity : 0.001 0.008 520 Dihedral : 4.320 11.753 390 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.50 % Allowed : 20.71 % Favored : 76.79 % 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: -2.64 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.008 0.001 PHE H 4 TYR 0.003 0.001 TYR C 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.335 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 1.7135 time to fit residues: 63.1048 Evaluate side-chains 33 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 0.0270 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2920 Z= 0.244 Angle : 0.458 3.955 3900 Z= 0.244 Chirality : 0.052 0.131 390 Planarity : 0.001 0.006 520 Dihedral : 4.399 12.154 390 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.14 % Allowed : 20.71 % Favored : 77.14 % 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: -2.64 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.009 0.001 PHE D 4 TYR 0.008 0.001 TYR I 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 29 time to evaluate : 0.337 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 34 average time/residue: 1.3968 time to fit residues: 48.7574 Evaluate side-chains 33 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0298 time to fit residues: 0.4662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 13 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2920 Z= 0.216 Angle : 0.438 3.977 3900 Z= 0.234 Chirality : 0.051 0.131 390 Planarity : 0.001 0.006 520 Dihedral : 4.279 12.960 390 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.14 % Allowed : 21.43 % Favored : 76.43 % 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: -2.61 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 13 PHE 0.009 0.001 PHE H 4 TYR 0.003 0.001 TYR A 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.333 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 1.2940 time to fit residues: 49.2281 Evaluate side-chains 33 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.319 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2920 Z= 0.364 Angle : 0.526 8.770 3900 Z= 0.272 Chirality : 0.052 0.132 390 Planarity : 0.002 0.007 520 Dihedral : 4.759 12.852 390 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.79 % Allowed : 21.43 % Favored : 76.79 % 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: -2.64 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 13 PHE 0.013 0.002 PHE D 4 TYR 0.007 0.002 TYR I 10 ARG 0.002 0.001 ARG H 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.313 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 1.5058 time to fit residues: 55.5283 Evaluate side-chains 33 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.0470 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.124225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.107242 restraints weight = 3786.417| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.66 r_work: 0.3829 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 2920 Z= 0.406 Angle : 0.567 8.443 3900 Z= 0.296 Chirality : 0.053 0.133 390 Planarity : 0.002 0.009 520 Dihedral : 4.930 12.935 390 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.43 % Allowed : 21.43 % Favored : 77.14 % 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: -2.68 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 13 PHE 0.014 0.002 PHE F 4 TYR 0.007 0.002 TYR I 10 ARG 0.002 0.001 ARG H 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1580.28 seconds wall clock time: 28 minutes 48.35 seconds (1728.35 seconds total)