Starting phenix.real_space_refine on Wed Jan 17 17:15:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/01_2024/8ol3_16944.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/01_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_16944/01_2024/8ol3_16944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/01_2024/8ol3_16944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/01_2024/8ol3_16944.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol3_16944/01_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 2.69, per 1000 atoms: 0.54 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: 3.93 Conformation dependent library (CDL) restraints added in 528.1 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: 0.67 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: 1.74 Time building geometry restraints manager: 4.09 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: 2164 34.66 - 69.32: 30 69.32 - 103.98: 10 103.98 - 138.64: 0 138.64 - 173.30: 6 Dihedral angle restraints: 2210 sinusoidal: 1120 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 2207 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: 1.830 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: 0.090 Extract box with map and model: 6.710 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 21.250 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- 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 : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1516 time to fit residues: 15.5271 Evaluate side-chains 36 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 1.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7799 moved from start: 0.2435 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= 0.135 Angle : 0.398 2.513 3380 Z= 0.234 Chirality : 0.059 0.148 390 Planarity : 0.001 0.005 430 Dihedral : 4.807 13.558 340 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.48 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: -0.22 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.16 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 14 PHE 0.009 0.001 PHE C 19 TYR 0.002 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 43 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 38 time to evaluate : 0.442 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: 43 average time/residue: 0.1580 time to fit residues: 9.3582 Evaluate side-chains 36 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 0.4980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2510 Z= 0.159 Angle : 0.393 3.553 3380 Z= 0.229 Chirality : 0.058 0.138 390 Planarity : 0.001 0.005 430 Dihedral : 5.223 16.168 340 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.00 % Allowed : 11.60 % 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: -0.22 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.16 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 13 PHE 0.009 0.002 PHE E 19 TYR 0.003 0.001 TYR J 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 46 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7496 (pt0) outliers start: 5 outliers final: 2 residues processed: 46 average time/residue: 0.1584 time to fit residues: 10.0080 Evaluate side-chains 38 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain H 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: 9.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 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: 0.7909 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2510 Z= 0.170 Angle : 0.389 2.957 3380 Z= 0.228 Chirality : 0.058 0.149 390 Planarity : 0.001 0.005 430 Dihedral : 5.585 19.108 340 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.80 % Allowed : 12.40 % 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: -0.28 (0.50), 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 0.003 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 41 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.430 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: 41 average time/residue: 0.1625 time to fit residues: 9.2208 Evaluate side-chains 38 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 40 VAL Chi-restraints excluded: chain H 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: 9.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 0.0170 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.9624 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.3658 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= 0.102 Angle : 0.366 4.424 3380 Z= 0.211 Chirality : 0.058 0.139 390 Planarity : 0.001 0.005 430 Dihedral : 5.076 16.215 340 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.60 % Allowed : 14.00 % 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: -0.35 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.25 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 13 PHE 0.007 0.001 PHE C 19 TYR 0.002 0.001 TYR H 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 40 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.390 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: 4 outliers final: 2 residues processed: 40 average time/residue: 0.1419 time to fit residues: 8.0247 Evaluate side-chains 36 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL 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: 6.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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** ** 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: 0.7995 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2510 Z= 0.252 Angle : 0.427 3.849 3380 Z= 0.252 Chirality : 0.058 0.159 390 Planarity : 0.002 0.009 430 Dihedral : 6.753 27.562 340 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.80 % Allowed : 13.60 % Favored : 83.60 % 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: -0.17 (0.50), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.12 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 13 PHE 0.015 0.002 PHE C 19 TYR 0.003 0.001 TYR F 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 41 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.421 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: 41 average time/residue: 0.1398 time to fit residues: 8.2110 Evaluate side-chains 39 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 40 VAL 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 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: 0.7980 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2510 Z= 0.105 Angle : 0.361 2.123 3380 Z= 0.210 Chirality : 0.058 0.143 390 Planarity : 0.001 0.005 430 Dihedral : 5.551 18.986 340 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.20 % Allowed : 16.80 % Favored : 82.00 % 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: -0.33 (0.49), 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 0.000 HIS C 13 PHE 0.006 0.001 PHE C 19 TYR 0.003 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 41 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.422 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: 3 outliers final: 3 residues processed: 41 average time/residue: 0.1424 time to fit residues: 8.3030 Evaluate side-chains 38 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 40 VAL 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: 8.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2510 Z= 0.215 Angle : 0.397 3.733 3380 Z= 0.233 Chirality : 0.057 0.147 390 Planarity : 0.002 0.011 430 Dihedral : 6.168 24.017 340 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.60 % Allowed : 15.60 % Favored : 80.80 % 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: -0.31 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.23 (0.37), 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 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 44 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.422 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: 43 average time/residue: 0.1493 time to fit residues: 9.2008 Evaluate side-chains 41 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 F residue 40 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.0870 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2510 Z= 0.113 Angle : 0.365 3.636 3380 Z= 0.211 Chirality : 0.058 0.140 390 Planarity : 0.001 0.007 430 Dihedral : 5.336 17.320 340 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.60 % Allowed : 18.40 % 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: -0.44 (0.49), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 14 PHE 0.006 0.001 PHE C 19 TYR 0.002 0.000 TYR J 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 39 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.477 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: 4 outliers final: 4 residues processed: 39 average time/residue: 0.1614 time to fit residues: 9.2008 Evaluate side-chains 38 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain H residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2510 Z= 0.297 Angle : 0.435 3.021 3380 Z= 0.257 Chirality : 0.057 0.151 390 Planarity : 0.002 0.010 430 Dihedral : 6.874 28.817 340 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.40 % Allowed : 16.80 % Favored : 80.80 % 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: -0.51 (0.48), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 13 PHE 0.016 0.003 PHE C 19 TYR 0.004 0.001 TYR D 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 40 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 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: 6 outliers final: 6 residues processed: 40 average time/residue: 0.1407 time to fit residues: 8.0946 Evaluate side-chains 40 residues out of total 250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 G residue 40 VAL Chi-restraints excluded: chain H 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: 5.9990 chunk 16 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.135801 restraints weight = 12568.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.141072 restraints weight = 5153.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.145050 restraints weight = 2901.803| |-----------------------------------------------------------------------------| r_work (final): 0.4784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4780 r_free = 0.4780 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4779 r_free = 0.4779 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4779 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2510 Z= 0.188 Angle : 0.393 3.192 3380 Z= 0.229 Chirality : 0.057 0.144 390 Planarity : 0.001 0.008 430 Dihedral : 6.443 26.060 340 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.40 % Allowed : 17.60 % 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: -0.60 (0.48), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.45 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.010 0.002 PHE C 19 TYR 0.003 0.001 TYR J 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.22 seconds wall clock time: 40 minutes 48.27 seconds (2448.27 seconds total)