Starting phenix.real_space_refine on Wed Jan 17 16:50:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv6_14168/01_2024/7qv6_14168.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv6_14168/01_2024/7qv6_14168.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/7qv6_14168/01_2024/7qv6_14168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv6_14168/01_2024/7qv6_14168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv6_14168/01_2024/7qv6_14168.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv6_14168/01_2024/7qv6_14168.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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 1512 2.51 5 N 378 2.21 5 O 396 1.98 5 H 2556 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4842 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "D" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "H" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "G" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "K" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "J" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "I" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "L" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "N" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "M" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "Q" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "P" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "O" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Chain: "R" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 269 Classifications: {'peptide': 17} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 16} Time building chain proxies: 2.26, per 1000 atoms: 0.47 Number of scatterers: 4842 At special positions: 0 Unit cell: (94.35, 78.2, 33.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 396 8.00 N 378 7.00 C 1512 6.00 H 2556 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: 3.25 Conformation dependent library (CDL) restraints added in 444.5 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 58.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 10 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 16 removed outlier: 6.582A pdb=" N ILE B 13 " --> pdb=" O VAL H 14 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N SER H 16 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER B 15 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 13 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N SER N 16 " --> pdb=" O ILE H 13 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER H 15 " --> pdb=" O SER N 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 2 through 8 removed outlier: 6.293A pdb=" N PHE A 3 " --> pdb=" O ASP G 4 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL G 6 " --> pdb=" O PHE A 3 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 5 " --> pdb=" O VAL G 6 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS G 8 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS A 7 " --> pdb=" O LYS G 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE G 3 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL M 6 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE G 5 " --> pdb=" O VAL M 6 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LYS M 8 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS G 7 " --> pdb=" O LYS M 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.322A pdb=" N ALA E 10 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA K 10 " --> pdb=" O GLY Q 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 2 through 16 removed outlier: 9.319A pdb=" N PHE D 3 " --> pdb=" O ASP J 4 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL J 6 " --> pdb=" O PHE D 3 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ILE D 5 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N LYS J 8 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N LYS D 7 " --> pdb=" O LYS J 8 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ALA J 10 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ILE D 9 " --> pdb=" O ALA J 10 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N HIS J 12 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLY D 11 " --> pdb=" O HIS J 12 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL J 14 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 13 " --> pdb=" O VAL J 14 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER J 16 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER D 15 " --> pdb=" O SER J 16 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N PHE J 3 " --> pdb=" O ASP P 4 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N VAL P 6 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ILE J 5 " --> pdb=" O VAL P 6 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N LYS P 8 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N LYS J 7 " --> pdb=" O LYS P 8 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ALA P 10 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ILE J 9 " --> pdb=" O ALA P 10 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N HIS P 12 " --> pdb=" O ILE J 9 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N GLY J 11 " --> pdb=" O HIS P 12 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL P 14 " --> pdb=" O GLY J 11 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE J 13 " --> pdb=" O VAL P 14 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N SER P 16 " --> pdb=" O ILE J 13 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER J 15 " --> pdb=" O SER P 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 15 removed outlier: 5.970A pdb=" N PHE C 3 " --> pdb=" O ASP I 4 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL I 6 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE C 5 " --> pdb=" O VAL I 6 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LYS I 8 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS C 7 " --> pdb=" O LYS I 8 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ALA I 10 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 9 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N HIS I 12 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N GLY C 11 " --> pdb=" O HIS I 12 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL I 14 " --> pdb=" O GLY C 11 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ILE C 13 " --> pdb=" O VAL I 14 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE I 3 " --> pdb=" O ASP O 4 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL O 6 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE I 5 " --> pdb=" O VAL O 6 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N LYS O 8 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS I 7 " --> pdb=" O LYS O 8 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ALA O 10 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE I 9 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N HIS O 12 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N GLY I 11 " --> pdb=" O HIS O 12 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL O 14 " --> pdb=" O GLY I 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N ILE I 13 " --> pdb=" O VAL O 14 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 15 46 hydrogen bonds defined for protein. 138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 2556 0.98 - 1.12: 0 1.12 - 1.26: 360 1.26 - 1.40: 486 1.40 - 1.54: 1458 Bond restraints: 4860 Sorted by residual: bond pdb=" CB VAL C 14 " pdb=" CG2 VAL C 14 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.01e+00 bond pdb=" CB VAL I 14 " pdb=" CG2 VAL I 14 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB VAL O 14 " pdb=" CG2 VAL O 14 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CG1 ILE F 13 " pdb=" CD1 ILE F 13 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 bond pdb=" CG1 ILE L 13 " pdb=" CD1 ILE L 13 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.74e+00 ... (remaining 4855 not shown) Histogram of bond angle deviations from ideal: 105.62 - 110.73: 5809 110.73 - 115.85: 1131 115.85 - 120.96: 909 120.96 - 126.08: 1013 126.08 - 131.19: 48 Bond angle restraints: 8910 Sorted by residual: angle pdb=" N GLY Q 11 " pdb=" CA GLY Q 11 " pdb=" C GLY Q 11 " ideal model delta sigma weight residual 110.45 114.94 -4.49 1.30e+00 5.92e-01 1.19e+01 angle pdb=" N GLY K 11 " pdb=" CA GLY K 11 " pdb=" C GLY K 11 " ideal model delta sigma weight residual 110.45 114.93 -4.48 1.30e+00 5.92e-01 1.19e+01 angle pdb=" N GLY E 11 " pdb=" CA GLY E 11 " pdb=" C GLY E 11 " ideal model delta sigma weight residual 110.45 114.93 -4.48 1.30e+00 5.92e-01 1.19e+01 angle pdb=" N GLY R 11 " pdb=" CA GLY R 11 " pdb=" C GLY R 11 " ideal model delta sigma weight residual 110.29 114.31 -4.02 1.28e+00 6.10e-01 9.84e+00 angle pdb=" N GLY F 11 " pdb=" CA GLY F 11 " pdb=" C GLY F 11 " ideal model delta sigma weight residual 110.29 114.31 -4.02 1.28e+00 6.10e-01 9.84e+00 ... (remaining 8905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.69: 1887 12.69 - 25.37: 113 25.37 - 38.06: 49 38.06 - 50.74: 39 50.74 - 63.43: 18 Dihedral angle restraints: 2106 sinusoidal: 1134 harmonic: 972 Sorted by residual: dihedral pdb=" CA ASP L 4 " pdb=" C ASP L 4 " pdb=" N ILE L 5 " pdb=" CA ILE L 5 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" CA ASP F 4 " pdb=" C ASP F 4 " pdb=" N ILE F 5 " pdb=" CA ILE F 5 " ideal model delta harmonic sigma weight residual 180.00 165.33 14.67 0 5.00e+00 4.00e-02 8.60e+00 dihedral pdb=" CA ASP R 4 " pdb=" C ASP R 4 " pdb=" N ILE R 5 " pdb=" CA ILE R 5 " ideal model delta harmonic sigma weight residual 180.00 165.35 14.65 0 5.00e+00 4.00e-02 8.59e+00 ... (remaining 2103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 141 0.024 - 0.047: 87 0.047 - 0.071: 66 0.071 - 0.094: 75 0.094 - 0.118: 27 Chirality restraints: 396 Sorted by residual: chirality pdb=" CA ILE Q 5 " pdb=" N ILE Q 5 " pdb=" C ILE Q 5 " pdb=" CB ILE Q 5 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE F 9 " pdb=" N ILE F 9 " pdb=" C ILE F 9 " pdb=" CB ILE F 9 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE L 9 " pdb=" N ILE L 9 " pdb=" C ILE L 9 " pdb=" CB ILE L 9 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 393 not shown) Planarity restraints: 648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS J 12 " 0.007 2.00e-02 2.50e+03 4.46e-03 4.48e-01 pdb=" CG HIS J 12 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS J 12 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS J 12 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS J 12 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS J 12 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS J 12 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS J 12 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS J 12 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS P 12 " 0.007 2.00e-02 2.50e+03 4.38e-03 4.31e-01 pdb=" CG HIS P 12 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS P 12 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS P 12 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS P 12 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS P 12 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS P 12 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS P 12 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS P 12 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 12 " 0.006 2.00e-02 2.50e+03 4.35e-03 4.26e-01 pdb=" CG HIS D 12 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS D 12 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 12 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 12 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS D 12 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 HIS D 12 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS D 12 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 HIS D 12 " 0.002 2.00e-02 2.50e+03 ... (remaining 645 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.45: 3232 2.45 - 2.97: 10383 2.97 - 3.48: 9111 3.48 - 3.99: 13759 3.99 - 4.50: 18178 Nonbonded interactions: 54663 Sorted by model distance: nonbonded pdb=" O GLY F 1 " pdb=" H2 GLY L 1 " model vdw 1.943 1.850 nonbonded pdb=" O GLY L 1 " pdb=" H2 GLY R 1 " model vdw 1.943 1.850 nonbonded pdb="HD23 LEU J 2 " pdb="HD13 LEU P 2 " model vdw 1.954 2.440 nonbonded pdb="HD23 LEU D 2 " pdb="HD13 LEU J 2 " model vdw 1.954 2.440 nonbonded pdb=" O PHE C 3 " pdb=" H ASP I 4 " model vdw 2.008 1.850 ... (remaining 54658 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' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.080 Extract box with map and model: 7.470 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.340 Find NCS groups from input model: 0.230 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.011 0.052 2304 Z= 0.711 Angle : 0.587 4.492 3078 Z= 0.355 Chirality : 0.054 0.118 396 Planarity : 0.001 0.005 360 Dihedral : 11.565 54.871 810 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.85 (0.39), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.30), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 12 PHE 0.008 0.002 PHE M 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.409 Fit side-chains REVERT: D 8 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8347 (ttmm) REVERT: J 8 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8292 (mtpp) REVERT: P 8 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8594 (mtpp) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.7372 time to fit residues: 16.9783 Evaluate side-chains 20 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 12 HIS Q 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2304 Z= 0.123 Angle : 0.399 2.777 3078 Z= 0.229 Chirality : 0.063 0.156 396 Planarity : 0.001 0.007 360 Dihedral : 7.707 43.629 306 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 2.38 % Favored : 96.83 % 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: -0.65 (0.45), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS R 12 PHE 0.004 0.001 PHE R 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.405 Fit side-chains REVERT: D 8 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8354 (ttmm) REVERT: J 8 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8351 (mtpp) REVERT: P 8 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8605 (mtpp) outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.5373 time to fit residues: 12.2273 Evaluate side-chains 20 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2304 Z= 0.119 Angle : 0.356 2.207 3078 Z= 0.200 Chirality : 0.062 0.148 396 Planarity : 0.001 0.005 360 Dihedral : 5.740 25.076 306 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 4.37 % Favored : 94.84 % 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: 0.14 (0.48), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.12 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.006 0.001 PHE J 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.398 Fit side-chains REVERT: D 8 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8019 (mttm) REVERT: J 8 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8362 (mtpp) REVERT: P 8 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8590 (mtpp) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.5976 time to fit residues: 14.7207 Evaluate side-chains 22 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2304 Z= 0.346 Angle : 0.423 3.231 3078 Z= 0.236 Chirality : 0.059 0.140 396 Planarity : 0.001 0.007 360 Dihedral : 7.205 42.411 306 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 5.56 % Favored : 93.65 % 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: 0.05 (0.48), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.05 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS Q 12 PHE 0.007 0.001 PHE A 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.380 Fit side-chains REVERT: D 8 LYS cc_start: 0.8517 (mtpt) cc_final: 0.7977 (mttm) REVERT: J 7 LYS cc_start: 0.8287 (mttt) cc_final: 0.8047 (mttp) REVERT: P 8 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8583 (mtpp) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.7522 time to fit residues: 17.2742 Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2304 Z= 0.111 Angle : 0.358 3.913 3078 Z= 0.197 Chirality : 0.062 0.145 396 Planarity : 0.001 0.004 360 Dihedral : 5.853 32.758 306 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 5.95 % Favored : 93.25 % 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: 0.36 (0.50), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.29 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.002 0.000 PHE E 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.402 Fit side-chains REVERT: D 8 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8037 (mttm) REVERT: J 7 LYS cc_start: 0.8265 (mttt) cc_final: 0.8019 (mttp) REVERT: P 8 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8580 (mtpp) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.6627 time to fit residues: 16.1194 Evaluate side-chains 22 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2304 Z= 0.129 Angle : 0.347 3.275 3078 Z= 0.191 Chirality : 0.062 0.144 396 Planarity : 0.001 0.004 360 Dihedral : 5.103 23.931 306 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 5.95 % Favored : 93.25 % 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: 0.50 (0.51), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.39 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS R 12 PHE 0.004 0.001 PHE E 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.422 Fit side-chains REVERT: D 8 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8030 (mttm) REVERT: P 8 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8523 (mtpp) outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.6597 time to fit residues: 16.0787 Evaluate side-chains 22 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2304 Z= 0.146 Angle : 0.356 3.267 3078 Z= 0.196 Chirality : 0.061 0.142 396 Planarity : 0.001 0.004 360 Dihedral : 5.133 24.546 306 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % 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: 0.52 (0.52), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.41 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Q 12 PHE 0.003 0.001 PHE E 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.372 Fit side-chains REVERT: D 8 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8024 (mttm) REVERT: P 8 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8521 (mtpp) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.6905 time to fit residues: 16.0893 Evaluate side-chains 22 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2304 Z= 0.145 Angle : 0.355 3.203 3078 Z= 0.195 Chirality : 0.061 0.142 396 Planarity : 0.001 0.004 360 Dihedral : 5.106 25.275 306 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 7.14 % Favored : 92.06 % 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: 0.53 (0.52), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.41 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 12 PHE 0.003 0.001 PHE E 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.357 Fit side-chains REVERT: D 8 LYS cc_start: 0.8490 (mtpt) cc_final: 0.8038 (mttm) REVERT: P 8 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8507 (mtpp) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.6873 time to fit residues: 16.4783 Evaluate side-chains 22 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2304 Z= 0.186 Angle : 0.367 3.128 3078 Z= 0.202 Chirality : 0.061 0.145 396 Planarity : 0.001 0.004 360 Dihedral : 5.570 31.931 306 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 7.54 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.52), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.33 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 12 PHE 0.004 0.001 PHE E 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.377 Fit side-chains REVERT: D 8 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8031 (mttm) REVERT: P 8 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8531 (mtpp) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.7398 time to fit residues: 17.0886 Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2304 Z= 0.121 Angle : 0.349 3.148 3078 Z= 0.191 Chirality : 0.062 0.143 396 Planarity : 0.001 0.004 360 Dihedral : 5.017 27.059 306 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 7.54 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.52), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.42 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.003 0.000 PHE E 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.409 Fit side-chains REVERT: D 8 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8064 (mttm) REVERT: P 8 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8494 (mtpp) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.7046 time to fit residues: 16.3430 Evaluate side-chains 22 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain K residue 4 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.135835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.112396 restraints weight = 9013.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.118967 restraints weight = 3800.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.122967 restraints weight = 2129.099| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.018 2304 Z= 0.091 Angle : 0.336 3.198 3078 Z= 0.183 Chirality : 0.062 0.140 396 Planarity : 0.001 0.004 360 Dihedral : 4.211 17.904 306 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 7.54 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.53), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.52 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 12 PHE 0.002 0.000 PHE E 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.12 seconds wall clock time: 32 minutes 15.63 seconds (1935.63 seconds total)