Starting phenix.real_space_refine on Sun Mar 10 20:51:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/03_2024/8ol3_16944.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/03_2024/8ol3_16944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/03_2024/8ol3_16944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/03_2024/8ol3_16944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/03_2024/8ol3_16944.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/03_2024/8ol3_16944.pdb" } resolution = 3.5 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= 0.280 sd= 1.397 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: 5 Type Number sf(0) Gaussians S 10 5.16 5 C 1610 2.51 5 N 410 2.21 5 O 440 1.98 5 H 2500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 4970 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "A" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "B" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "D" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "F" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "G" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "H" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "I" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "J" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 497 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Time building chain proxies: 2.33, per 1000 atoms: 0.47 Number of scatterers: 4970 At special positions: 0 Unit cell: (61.2, 90.576, 39.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 O 440 8.00 N 410 7.00 C 1610 6.00 H 2500 1.00 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: 4.07 Conformation dependent library (CDL) restraints added in 548.6 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 60.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 21 removed outlier: 7.049A pdb=" N VAL C 12 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N HIS A 13 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N HIS C 14 " --> pdb=" O HIS A 13 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL E 12 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS C 13 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS E 14 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N GLU E 11 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N HIS G 14 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N HIS E 13 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N LYS G 16 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN E 15 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL G 18 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE G 20 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE E 19 " --> pdb=" O PHE G 20 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N GLU G 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS I 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS G 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LYS I 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN G 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL I 18 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE I 20 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE G 19 " --> pdb=" O PHE I 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 27 removed outlier: 8.596A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN C 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N SER A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER C 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN E 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL E 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN G 27 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N SER E 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N VAL G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASN I 27 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N SER G 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 35 removed outlier: 6.212A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU E 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET C 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU G 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLY E 33 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU I 34 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY G 33 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.447A pdb=" N VAL E 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 21 removed outlier: 9.222A pdb=" N GLU B 11 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N HIS D 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS B 13 " --> pdb=" O HIS D 14 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LYS D 16 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN B 15 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL D 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE D 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE B 19 " --> pdb=" O PHE D 20 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N GLU D 11 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N HIS F 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS D 13 " --> pdb=" O HIS F 14 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LYS F 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN D 15 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL F 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N PHE F 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE D 19 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N GLU F 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N HIS H 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS F 13 " --> pdb=" O HIS H 14 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LYS H 16 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN F 15 " --> pdb=" O LYS H 16 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL H 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N PHE H 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE F 19 " --> pdb=" O PHE H 20 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLU H 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N HIS J 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N HIS H 13 " --> pdb=" O HIS J 14 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS J 16 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN H 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL J 18 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU H 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE J 20 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE H 19 " --> pdb=" O PHE J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 24 through 27 removed outlier: 8.627A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ASN D 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N SER B 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASN F 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N SER D 26 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N VAL F 24 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASN H 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N SER F 26 " --> pdb=" O ASN H 27 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N VAL H 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASN J 27 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N SER H 26 " --> pdb=" O ASN J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 35 removed outlier: 6.242A pdb=" N ILE B 31 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU D 34 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY B 33 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE D 31 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU F 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLY D 33 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE F 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU H 34 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY F 33 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE H 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU J 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLY H 33 " --> pdb=" O LEU J 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 41 32 hydrogen bonds defined for protein. 96 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: 1.54 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 1.05: 2494 1.05 - 1.41: 1050 1.41 - 1.77: 1442 1.77 - 2.13: 22 2.13 - 2.49: 2 Bond restraints: 5010 Sorted by residual: bond pdb=" CE1 HIS H 13 " pdb=" HE1 HIS H 13 " ideal model delta sigma weight residual 0.930 2.489 -1.559 2.00e-02 2.50e+03 6.08e+03 bond pdb=" CE1 HIS A 13 " pdb=" HE1 HIS A 13 " ideal model delta sigma weight residual 0.930 2.489 -1.559 2.00e-02 2.50e+03 6.08e+03 bond pdb=" CD2 HIS H 13 " pdb=" HD2 HIS H 13 " ideal model delta sigma weight residual 0.930 1.940 -1.010 2.00e-02 2.50e+03 2.55e+03 bond pdb=" CD2 HIS A 13 " pdb=" HD2 HIS A 13 " ideal model delta sigma weight residual 0.930 1.939 -1.009 2.00e-02 2.50e+03 2.54e+03 bond pdb=" NE2 HIS H 13 " pdb=" HE2 HIS H 13 " ideal model delta sigma weight residual 0.860 1.562 -0.702 2.00e-02 2.50e+03 1.23e+03 ... (remaining 5005 not shown) Histogram of bond angle deviations from ideal: 15.98 - 43.55: 14 43.55 - 71.13: 0 71.13 - 98.70: 20 98.70 - 126.27: 8961 126.27 - 153.85: 65 Bond angle restraints: 9060 Sorted by residual: angle pdb=" CG HIS H 13 " pdb=" CD2 HIS H 13 " pdb=" HD2 HIS H 13 " ideal model delta sigma weight residual 126.40 15.98 110.42 3.00e+00 1.11e-01 1.35e+03 angle pdb=" CG HIS A 13 " pdb=" CD2 HIS A 13 " pdb=" HD2 HIS A 13 " ideal model delta sigma weight residual 126.40 16.06 110.34 3.00e+00 1.11e-01 1.35e+03 angle pdb=" NE2 HIS A 13 " pdb=" CE1 HIS A 13 " pdb=" HE1 HIS A 13 " ideal model delta sigma weight residual 125.80 26.93 98.87 3.00e+00 1.11e-01 1.09e+03 angle pdb=" NE2 HIS H 13 " pdb=" CE1 HIS H 13 " pdb=" HE1 HIS H 13 " ideal model delta sigma weight residual 125.80 26.94 98.86 3.00e+00 1.11e-01 1.09e+03 angle pdb=" CE1 HIS H 13 " pdb=" NE2 HIS H 13 " pdb=" HE2 HIS H 13 " ideal model delta sigma weight residual 125.50 32.75 92.75 3.00e+00 1.11e-01 9.56e+02 ... (remaining 9055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.66: 2204 34.66 - 69.32: 90 69.32 - 103.98: 10 103.98 - 138.64: 0 138.64 - 173.30: 6 Dihedral angle restraints: 2310 sinusoidal: 1220 harmonic: 1090 Sorted by residual: dihedral pdb=" CG HIS A 13 " pdb=" ND1 HIS A 13 " pdb=" CE1 HIS A 13 " pdb=" HE1 HIS A 13 " ideal model delta harmonic sigma weight residual -180.00 -6.70 -173.30 0 5.00e+00 4.00e-02 1.20e+03 dihedral pdb=" CG HIS H 13 " pdb=" ND1 HIS H 13 " pdb=" CE1 HIS H 13 " pdb=" HE1 HIS H 13 " ideal model delta harmonic sigma weight residual -180.00 -6.74 -173.26 0 5.00e+00 4.00e-02 1.20e+03 dihedral pdb=" ND1 HIS A 13 " pdb=" CG HIS A 13 " pdb=" CD2 HIS A 13 " pdb=" HD2 HIS A 13 " ideal model delta harmonic sigma weight residual -180.00 -10.02 -169.98 0 5.00e+00 4.00e-02 1.16e+03 ... (remaining 2307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 221 0.027 - 0.054: 66 0.054 - 0.081: 20 0.081 - 0.108: 33 0.108 - 0.135: 50 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA ILE H 31 " pdb=" N ILE H 31 " pdb=" C ILE H 31 " pdb=" CB ILE H 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-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 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 387 not shown) Planarity restraints: 750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 13 " -0.004 2.00e-02 2.50e+03 5.59e-02 7.03e+01 pdb=" CG HIS I 13 " 0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS I 13 " -0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS I 13 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 HIS I 13 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 HIS I 13 " 0.065 2.00e-02 2.50e+03 pdb=" HD1 HIS I 13 " 0.090 2.00e-02 2.50e+03 pdb=" HD2 HIS I 13 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS I 13 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 13 " 0.004 2.00e-02 2.50e+03 5.58e-02 7.01e+01 pdb=" CG HIS H 13 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS H 13 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS H 13 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 HIS H 13 " -0.032 2.00e-02 2.50e+03 pdb=" NE2 HIS H 13 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 HIS H 13 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 HIS H 13 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 HIS H 13 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS J 13 " 0.004 2.00e-02 2.50e+03 5.58e-02 6.99e+01 pdb=" CG HIS J 13 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS J 13 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS J 13 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 HIS J 13 " -0.032 2.00e-02 2.50e+03 pdb=" NE2 HIS J 13 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 HIS J 13 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 HIS J 13 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 HIS J 13 " 0.026 2.00e-02 2.50e+03 ... (remaining 747 not shown) Histogram of nonbonded interaction distances: 0.70 - 1.48: 4 1.48 - 2.26: 798 2.26 - 3.04: 14695 3.04 - 3.82: 20544 3.82 - 4.60: 33802 Warning: very small nonbonded interaction distances. Nonbonded interactions: 69843 Sorted by model distance: nonbonded pdb=" CD2 HIS A 13 " pdb=" HE1 HIS A 13 " model vdw 0.696 2.240 nonbonded pdb=" CD2 HIS H 13 " pdb=" HE1 HIS H 13 " model vdw 0.696 2.240 nonbonded pdb=" ND1 HIS A 13 " pdb=" HD2 HIS A 13 " model vdw 0.836 2.080 nonbonded pdb=" ND1 HIS H 13 " pdb=" HD2 HIS H 13 " model vdw 0.837 2.080 nonbonded pdb=" H HIS H 14 " pdb=" O HIS J 14 " model vdw 1.688 1.850 ... (remaining 69838 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.070 Extract box with map and model: 6.520 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.040 Find NCS groups from input model: 0.250 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.009 0.098 2510 Z= 0.556 Angle : 0.671 5.540 3380 Z= 0.579 Chirality : 0.057 0.135 390 Planarity : 0.008 0.052 430 Dihedral : 9.518 37.061 850 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: -0.18 (0.48), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.13 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.069 0.023 HIS G 13 PHE 0.003 0.001 PHE J 19 TYR 0.003 0.001 TYR I 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1508 time to fit residues: 15.4169 Evaluate side-chains 36 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7814 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2510 Z= 0.147 Angle : 0.404 2.568 3380 Z= 0.239 Chirality : 0.059 0.149 390 Planarity : 0.001 0.006 430 Dihedral : 4.918 13.583 340 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.00 % Allowed : 13.20 % Favored : 84.80 % 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: -0.24 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.17 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 14 PHE 0.010 0.001 PHE C 19 TYR 0.003 0.001 TYR I 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.1496 time to fit residues: 9.0870 Evaluate side-chains 37 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2510 Z= 0.199 Angle : 0.413 2.836 3380 Z= 0.243 Chirality : 0.058 0.140 390 Planarity : 0.002 0.006 430 Dihedral : 5.947 21.426 340 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.80 % Allowed : 10.80 % Favored : 86.40 % 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: -0.20 (0.50), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.14 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 13 PHE 0.013 0.002 PHE E 19 TYR 0.003 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1543 time to fit residues: 10.1886 Evaluate side-chains 39 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 HIS ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2510 Z= 0.171 Angle : 0.392 2.520 3380 Z= 0.231 Chirality : 0.058 0.150 390 Planarity : 0.001 0.007 430 Dihedral : 5.902 21.097 340 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.60 % Allowed : 12.00 % Favored : 84.40 % 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: -0.25 (0.50), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 13 PHE 0.010 0.002 PHE C 19 TYR 0.003 0.001 TYR H 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.1512 time to fit residues: 9.1044 Evaluate side-chains 40 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 2510 Z= 0.109 Angle : 0.364 2.033 3380 Z= 0.212 Chirality : 0.058 0.139 390 Planarity : 0.001 0.005 430 Dihedral : 5.288 16.663 340 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.80 % Allowed : 14.00 % Favored : 83.20 % 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: -0.32 (0.50), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.24 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS F 14 PHE 0.007 0.001 PHE C 19 TYR 0.003 0.001 TYR F 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 37 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.1467 time to fit residues: 9.0385 Evaluate side-chains 38 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2510 Z= 0.216 Angle : 0.400 2.753 3380 Z= 0.237 Chirality : 0.057 0.153 390 Planarity : 0.002 0.008 430 Dihedral : 6.193 23.906 340 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.00 % Allowed : 13.20 % Favored : 82.80 % 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: -0.27 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.012 0.002 PHE C 19 TYR 0.003 0.001 TYR J 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 43 average time/residue: 0.1387 time to fit residues: 8.5571 Evaluate side-chains 42 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 2510 Z= 0.103 Angle : 0.358 1.911 3380 Z= 0.208 Chirality : 0.058 0.138 390 Planarity : 0.001 0.005 430 Dihedral : 5.231 16.469 340 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.20 % Allowed : 17.60 % Favored : 81.20 % 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: -0.40 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.29 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.006 0.001 PHE C 19 TYR 0.002 0.001 TYR J 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.1434 time to fit residues: 7.9597 Evaluate side-chains 35 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2510 Z= 0.181 Angle : 0.383 2.446 3380 Z= 0.224 Chirality : 0.058 0.143 390 Planarity : 0.001 0.009 430 Dihedral : 5.735 20.828 340 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.00 % Allowed : 17.60 % Favored : 80.40 % 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: -0.39 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.29 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 13 PHE 0.010 0.002 PHE C 19 TYR 0.003 0.001 TYR J 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.1420 time to fit residues: 7.6341 Evaluate side-chains 37 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 2510 Z= 0.107 Angle : 0.357 1.822 3380 Z= 0.207 Chirality : 0.058 0.139 390 Planarity : 0.001 0.006 430 Dihedral : 5.141 16.261 340 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.20 % Allowed : 18.40 % Favored : 80.40 % 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: -0.48 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 14 PHE 0.006 0.001 PHE C 19 TYR 0.002 0.001 TYR I 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.1504 time to fit residues: 7.6600 Evaluate side-chains 36 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain J residue 11 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2510 Z= 0.325 Angle : 0.448 3.062 3380 Z= 0.267 Chirality : 0.057 0.150 390 Planarity : 0.002 0.010 430 Dihedral : 7.169 30.652 340 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.00 % Allowed : 18.00 % 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: -0.48 (0.48), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.016 0.003 PHE C 19 TYR 0.005 0.001 TYR J 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 0.1377 time to fit residues: 7.7323 Evaluate side-chains 36 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0470 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.173269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.145779 restraints weight = 13410.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.151485 restraints weight = 5935.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.156076 restraints weight = 3586.494| |-----------------------------------------------------------------------------| r_work (final): 0.4850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4895 r_free = 0.4895 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4893 r_free = 0.4893 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2510 Z= 0.112 Angle : 0.373 2.199 3380 Z= 0.216 Chirality : 0.058 0.138 390 Planarity : 0.001 0.006 430 Dihedral : 5.745 21.196 340 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.60 % Allowed : 18.80 % Favored : 79.60 % 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: -0.61 (0.48), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 14 PHE 0.006 0.001 PHE C 19 TYR 0.004 0.001 TYR J 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2269.26 seconds wall clock time: 40 minutes 38.56 seconds (2438.56 seconds total)