Starting phenix.real_space_refine on Fri Apr 5 21:01:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/04_2024/8sel_40421_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/04_2024/8sel_40421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/04_2024/8sel_40421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/04_2024/8sel_40421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/04_2024/8sel_40421_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/04_2024/8sel_40421_neut.pdb" } resolution = 3.8 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= 0.010 sd= 0.297 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3510 2.51 5 N 940 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5500 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "B" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "D" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "F" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "G" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "H" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "I" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "J" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "K" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "L" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "M" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "N" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "O" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "P" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "Q" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "R" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "S" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "T" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Time building chain proxies: 3.48, per 1000 atoms: 0.63 Number of scatterers: 5500 At special positions: 0 Unit cell: (152.83, 60.078, 41.106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1030 8.00 N 940 7.00 C 3510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.365A pdb=" N TYR A 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N HIS E 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR E 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N HIS I 13 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL E 12 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR I 10 " --> pdb=" O GLU M 11 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N HIS M 13 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL I 12 " --> pdb=" O HIS M 13 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR M 10 " --> pdb=" O GLU Q 11 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N HIS Q 13 " --> pdb=" O TYR M 10 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL M 12 " --> pdb=" O HIS Q 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 26 removed outlier: 7.972A pdb=" N VAL A 24 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL I 24 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL M 24 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.930A pdb=" N ILE E 31 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY E 33 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE I 31 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE E 32 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY I 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE M 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE I 32 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY M 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE Q 31 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE M 32 " --> pdb=" O ILE Q 31 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY Q 33 " --> pdb=" O ILE M 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 21 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 36 removed outlier: 6.896A pdb=" N ALA B 30 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE F 31 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY F 33 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA F 30 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE J 31 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE F 32 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY J 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA J 30 " --> pdb=" O GLY N 29 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE N 31 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE J 32 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY N 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA N 30 " --> pdb=" O GLY R 29 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE R 31 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE N 32 " --> pdb=" O ILE R 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY R 33 " --> pdb=" O ILE N 32 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.353A pdb=" N TYR C 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS G 13 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR G 10 " --> pdb=" O GLU K 11 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS K 13 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL G 12 " --> pdb=" O HIS K 13 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR K 10 " --> pdb=" O GLU O 11 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS O 13 " --> pdb=" O TYR K 10 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL K 12 " --> pdb=" O HIS O 13 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR O 10 " --> pdb=" O GLU S 11 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS S 13 " --> pdb=" O TYR O 10 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL O 12 " --> pdb=" O HIS S 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 21 Processing sheet with id=AB2, first strand: chain 'C' and resid 24 through 26 removed outlier: 7.962A pdb=" N VAL C 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL G 24 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL K 24 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL O 24 " --> pdb=" O GLY S 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 30 through 36 removed outlier: 6.914A pdb=" N ILE G 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY G 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE K 31 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE G 32 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY K 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE O 31 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE K 32 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY O 33 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE S 31 " --> pdb=" O ALA O 30 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE O 32 " --> pdb=" O ILE S 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY S 33 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 21 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 36 removed outlier: 6.884A pdb=" N ALA D 30 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE H 31 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE D 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY H 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA H 30 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE L 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE H 32 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY L 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA L 30 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE P 31 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE L 32 " --> pdb=" O ILE P 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY P 33 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA P 30 " --> pdb=" O GLY T 29 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE T 31 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE P 32 " --> pdb=" O ILE T 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY T 33 " --> pdb=" O ILE P 32 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 528 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: 1.41 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.31: 1228 1.31 - 1.43: 1272 1.43 - 1.54: 2932 1.54 - 1.66: 128 1.66 - 1.78: 40 Bond restraints: 5600 Sorted by residual: bond pdb=" CG GLN N 15 " pdb=" CD GLN N 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.07e+01 bond pdb=" CG GLN R 15 " pdb=" CD GLN R 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.07e+01 bond pdb=" CG GLN F 15 " pdb=" CD GLN F 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.06e+01 bond pdb=" CG GLN B 15 " pdb=" CD GLN B 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.04e+01 bond pdb=" CG GLN D 15 " pdb=" CD GLN D 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.04e+01 ... (remaining 5595 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.00: 80 106.00 - 112.39: 2550 112.39 - 118.77: 1943 118.77 - 125.16: 2836 125.16 - 131.55: 111 Bond angle restraints: 7520 Sorted by residual: angle pdb=" N HIS E 13 " pdb=" CA HIS E 13 " pdb=" C HIS E 13 " ideal model delta sigma weight residual 108.79 120.11 -11.32 1.53e+00 4.27e-01 5.47e+01 angle pdb=" N HIS O 13 " pdb=" CA HIS O 13 " pdb=" C HIS O 13 " ideal model delta sigma weight residual 108.79 120.10 -11.31 1.53e+00 4.27e-01 5.47e+01 angle pdb=" N HIS S 13 " pdb=" CA HIS S 13 " pdb=" C HIS S 13 " ideal model delta sigma weight residual 108.79 120.09 -11.30 1.53e+00 4.27e-01 5.46e+01 angle pdb=" N HIS M 13 " pdb=" CA HIS M 13 " pdb=" C HIS M 13 " ideal model delta sigma weight residual 108.79 120.09 -11.30 1.53e+00 4.27e-01 5.45e+01 angle pdb=" N HIS Q 13 " pdb=" CA HIS Q 13 " pdb=" C HIS Q 13 " ideal model delta sigma weight residual 108.79 120.09 -11.30 1.53e+00 4.27e-01 5.45e+01 ... (remaining 7515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2970 17.47 - 34.93: 110 34.93 - 52.40: 30 52.40 - 69.87: 0 69.87 - 87.33: 20 Dihedral angle restraints: 3130 sinusoidal: 1180 harmonic: 1950 Sorted by residual: dihedral pdb=" N HIS F 13 " pdb=" C HIS F 13 " pdb=" CA HIS F 13 " pdb=" CB HIS F 13 " ideal model delta harmonic sigma weight residual 122.80 130.46 -7.66 0 2.50e+00 1.60e-01 9.38e+00 dihedral pdb=" N HIS H 13 " pdb=" C HIS H 13 " pdb=" CA HIS H 13 " pdb=" CB HIS H 13 " ideal model delta harmonic sigma weight residual 122.80 130.41 -7.61 0 2.50e+00 1.60e-01 9.26e+00 dihedral pdb=" N HIS B 13 " pdb=" C HIS B 13 " pdb=" CA HIS B 13 " pdb=" CB HIS B 13 " ideal model delta harmonic sigma weight residual 122.80 130.41 -7.61 0 2.50e+00 1.60e-01 9.26e+00 ... (remaining 3127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 518 0.102 - 0.203: 232 0.203 - 0.305: 26 0.305 - 0.406: 24 0.406 - 0.508: 10 Chirality restraints: 810 Sorted by residual: chirality pdb=" CA HIS F 13 " pdb=" N HIS F 13 " pdb=" C HIS F 13 " pdb=" CB HIS F 13 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA HIS B 13 " pdb=" N HIS B 13 " pdb=" C HIS B 13 " pdb=" CB HIS B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CA HIS J 13 " pdb=" N HIS J 13 " pdb=" C HIS J 13 " pdb=" CB HIS J 13 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 807 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL O 40 " -0.025 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C VAL O 40 " 0.086 2.00e-02 2.50e+03 pdb=" O VAL O 40 " -0.031 2.00e-02 2.50e+03 pdb=" OXT VAL O 40 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 40 " -0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C VAL K 40 " 0.086 2.00e-02 2.50e+03 pdb=" O VAL K 40 " -0.031 2.00e-02 2.50e+03 pdb=" OXT VAL K 40 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL M 40 " -0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C VAL M 40 " 0.086 2.00e-02 2.50e+03 pdb=" O VAL M 40 " -0.031 2.00e-02 2.50e+03 pdb=" OXT VAL M 40 " -0.031 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 3029 2.96 - 3.44: 5294 3.44 - 3.93: 8855 3.93 - 4.41: 11486 4.41 - 4.90: 20185 Nonbonded interactions: 48849 Sorted by model distance: nonbonded pdb=" O HIS N 13 " pdb=" N GLN N 15 " model vdw 2.474 2.520 nonbonded pdb=" O HIS D 13 " pdb=" N GLN D 15 " model vdw 2.475 2.520 nonbonded pdb=" O HIS T 13 " pdb=" N GLN T 15 " model vdw 2.475 2.520 nonbonded pdb=" O HIS L 13 " pdb=" N GLN L 15 " model vdw 2.475 2.520 nonbonded pdb=" O HIS B 13 " pdb=" N GLN B 15 " model vdw 2.475 2.520 ... (remaining 48844 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } 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: 1.380 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: 0.010 Extract box with map and model: 5.570 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.260 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.026 0.159 5600 Z= 1.721 Angle : 2.245 12.963 7520 Z= 1.380 Chirality : 0.132 0.508 810 Planarity : 0.010 0.050 990 Dihedral : 12.887 87.332 1910 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 2.90 % Allowed : 4.35 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 13 PHE 0.017 0.006 PHE R 19 TYR 0.029 0.010 TYR R 10 ARG 0.001 0.000 ARG T 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 VAL cc_start: 0.8272 (t) cc_final: 0.8001 (m) REVERT: D 24 VAL cc_start: 0.8182 (t) cc_final: 0.7958 (m) REVERT: M 34 LEU cc_start: 0.8312 (tp) cc_final: 0.8064 (tp) REVERT: N 16 LYS cc_start: 0.7781 (tttt) cc_final: 0.7459 (mmtm) REVERT: Q 26 SER cc_start: 0.8867 (t) cc_final: 0.8562 (m) REVERT: S 26 SER cc_start: 0.8852 (t) cc_final: 0.8416 (m) REVERT: S 27 ASN cc_start: 0.7148 (t0) cc_final: 0.6548 (p0) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1523 time to fit residues: 44.4941 Evaluate side-chains 158 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS D 14 HIS F 14 HIS H 14 HIS J 14 HIS L 14 HIS N 14 HIS P 14 HIS Q 15 GLN R 14 HIS ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN T 14 HIS ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5600 Z= 0.316 Angle : 0.896 7.811 7520 Z= 0.492 Chirality : 0.063 0.213 810 Planarity : 0.004 0.019 990 Dihedral : 11.537 71.823 760 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 1.16 % Allowed : 10.43 % Favored : 88.41 % Rotamer: Outliers : 4.46 % Allowed : 14.46 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS R 14 PHE 0.017 0.003 PHE O 19 TYR 0.011 0.002 TYR J 10 ARG 0.001 0.000 ARG L 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 0.639 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: B 10 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.6512 (p90) REVERT: B 22 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6679 (pm20) REVERT: D 10 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.6508 (p90) REVERT: D 22 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6598 (pm20) REVERT: E 34 LEU cc_start: 0.8428 (tp) cc_final: 0.8195 (tp) REVERT: F 10 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.6506 (p90) REVERT: H 10 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.6542 (p90) REVERT: H 16 LYS cc_start: 0.7627 (mmtm) cc_final: 0.7310 (mmtm) REVERT: J 10 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7035 (p90) REVERT: L 10 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.6995 (p90) REVERT: R 5 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7072 (tpp-160) REVERT: R 7 ASP cc_start: 0.8044 (t0) cc_final: 0.7798 (t70) REVERT: R 27 ASN cc_start: 0.7378 (t0) cc_final: 0.5454 (p0) REVERT: S 26 SER cc_start: 0.8634 (t) cc_final: 0.8257 (m) REVERT: T 5 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7113 (tpp-160) REVERT: T 7 ASP cc_start: 0.7971 (t0) cc_final: 0.7722 (t70) REVERT: T 27 ASN cc_start: 0.7356 (t0) cc_final: 0.5473 (p0) outliers start: 25 outliers final: 5 residues processed: 200 average time/residue: 0.1747 time to fit residues: 44.8815 Evaluate side-chains 181 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain T residue 10 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.083 5600 Z= 0.653 Angle : 1.104 10.844 7520 Z= 0.614 Chirality : 0.073 0.251 810 Planarity : 0.005 0.020 990 Dihedral : 11.163 82.005 760 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 30.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 8.04 % Allowed : 19.82 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 13 PHE 0.031 0.005 PHE Q 19 TYR 0.016 0.003 TYR G 10 ARG 0.001 0.000 ARG J 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 198 time to evaluate : 0.643 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: symmetry clash REVERT: A 13 HIS cc_start: 0.7358 (p90) cc_final: 0.7007 (p90) REVERT: B 10 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.6891 (p90) REVERT: C 13 HIS cc_start: 0.7315 (p90) cc_final: 0.6872 (p90) REVERT: D 10 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7161 (p90) REVERT: E 34 LEU cc_start: 0.8467 (tp) cc_final: 0.8204 (tp) REVERT: F 10 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.6650 (p90) REVERT: G 13 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6791 (p90) REVERT: H 10 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.6610 (p90) REVERT: I 19 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6818 (p90) REVERT: J 10 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.7444 (p90) REVERT: K 19 PHE cc_start: 0.7281 (OUTLIER) cc_final: 0.6796 (p90) REVERT: L 10 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.7460 (p90) REVERT: L 27 ASN cc_start: 0.8738 (t0) cc_final: 0.8455 (t0) REVERT: M 13 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.6852 (p90) REVERT: N 10 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7445 (p90) REVERT: N 32 ILE cc_start: 0.8685 (mt) cc_final: 0.8450 (mt) REVERT: N 35 MET cc_start: 0.7256 (ttm) cc_final: 0.6982 (ttm) REVERT: O 28 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8662 (mtpp) REVERT: P 10 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.7536 (p90) REVERT: P 35 MET cc_start: 0.7253 (ttm) cc_final: 0.6993 (ttm) REVERT: Q 19 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6556 (p90) REVERT: R 5 ARG cc_start: 0.8475 (mtp180) cc_final: 0.7038 (tpp-160) REVERT: R 27 ASN cc_start: 0.8217 (t0) cc_final: 0.6913 (p0) REVERT: S 19 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6521 (p90) REVERT: S 26 SER cc_start: 0.8935 (t) cc_final: 0.8686 (m) REVERT: T 5 ARG cc_start: 0.8435 (mtp180) cc_final: 0.7125 (tpp-160) REVERT: T 7 ASP cc_start: 0.7816 (t0) cc_final: 0.7596 (t0) REVERT: T 27 ASN cc_start: 0.8177 (t0) cc_final: 0.6920 (p0) outliers start: 45 outliers final: 16 residues processed: 226 average time/residue: 0.1714 time to fit residues: 49.3684 Evaluate side-chains 215 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain T residue 10 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5600 Z= 0.344 Angle : 0.877 10.574 7520 Z= 0.482 Chirality : 0.063 0.194 810 Planarity : 0.003 0.016 990 Dihedral : 10.993 83.691 760 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 8.21 % Allowed : 21.96 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 13 PHE 0.025 0.003 PHE S 19 TYR 0.010 0.002 TYR J 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 191 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7235 (p90) cc_final: 0.6931 (p-80) REVERT: A 19 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6604 (p90) REVERT: B 10 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.6657 (p90) REVERT: C 13 HIS cc_start: 0.7241 (p90) cc_final: 0.6920 (p-80) REVERT: C 19 PHE cc_start: 0.6779 (OUTLIER) cc_final: 0.6453 (p90) REVERT: D 10 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.6693 (p90) REVERT: E 13 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.6592 (p90) REVERT: F 10 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.6360 (p90) REVERT: F 22 GLU cc_start: 0.8382 (tp30) cc_final: 0.8078 (tp30) REVERT: G 13 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6550 (p90) REVERT: H 7 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: H 10 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.6339 (p90) REVERT: H 36 VAL cc_start: 0.8574 (p) cc_final: 0.8194 (m) REVERT: I 13 HIS cc_start: 0.7170 (OUTLIER) cc_final: 0.6662 (p90) REVERT: I 19 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6375 (p90) REVERT: I 35 MET cc_start: 0.7770 (mmm) cc_final: 0.7524 (mmm) REVERT: J 10 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7202 (p90) REVERT: K 13 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.6722 (p90) REVERT: K 19 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.6313 (p90) REVERT: L 10 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7253 (p90) REVERT: M 13 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6613 (p90) REVERT: M 34 LEU cc_start: 0.8277 (tp) cc_final: 0.7984 (tp) REVERT: N 10 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7268 (p90) REVERT: O 34 LEU cc_start: 0.8290 (tp) cc_final: 0.8064 (tp) REVERT: P 10 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7289 (p90) REVERT: P 34 LEU cc_start: 0.9254 (tt) cc_final: 0.9038 (tp) REVERT: S 26 SER cc_start: 0.8870 (t) cc_final: 0.8650 (m) REVERT: T 35 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5630 (ttm) outliers start: 46 outliers final: 19 residues processed: 218 average time/residue: 0.1587 time to fit residues: 44.8142 Evaluate side-chains 216 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 35 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5600 Z= 0.256 Angle : 0.807 8.876 7520 Z= 0.438 Chirality : 0.061 0.203 810 Planarity : 0.003 0.013 990 Dihedral : 10.885 86.277 760 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 8.39 % Allowed : 22.86 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS P 13 PHE 0.021 0.003 PHE Q 19 TYR 0.011 0.001 TYR J 10 ARG 0.001 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 192 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7112 (p90) cc_final: 0.6747 (p-80) REVERT: B 10 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.6649 (p90) REVERT: C 13 HIS cc_start: 0.7111 (p90) cc_final: 0.6877 (p-80) REVERT: C 19 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6403 (p90) REVERT: D 10 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.6572 (p90) REVERT: E 13 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6691 (p90) REVERT: F 10 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6429 (p90) REVERT: H 7 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: H 10 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6414 (p90) REVERT: J 10 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7336 (p90) REVERT: K 19 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.6145 (p90) REVERT: Q 35 MET cc_start: 0.7845 (mmm) cc_final: 0.7477 (mmt) REVERT: S 15 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7110 (tm130) REVERT: S 17 LEU cc_start: 0.7469 (tp) cc_final: 0.7248 (tt) REVERT: S 26 SER cc_start: 0.8805 (t) cc_final: 0.8560 (m) REVERT: T 14 HIS cc_start: 0.6650 (OUTLIER) cc_final: 0.6421 (t-90) outliers start: 47 outliers final: 25 residues processed: 214 average time/residue: 0.1474 time to fit residues: 42.1685 Evaluate side-chains 213 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 0.0470 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 0.0570 chunk 7 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.6742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5600 Z= 0.368 Angle : 0.876 9.119 7520 Z= 0.476 Chirality : 0.065 0.259 810 Planarity : 0.003 0.016 990 Dihedral : 11.179 89.431 760 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 10.36 % Allowed : 22.68 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 13 PHE 0.034 0.004 PHE I 19 TYR 0.009 0.001 TYR J 10 ARG 0.002 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 181 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7337 (p90) cc_final: 0.6902 (p-80) REVERT: A 19 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6617 (p90) REVERT: B 10 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.6690 (p90) REVERT: C 13 HIS cc_start: 0.7248 (p90) cc_final: 0.6855 (p-80) REVERT: C 19 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6524 (p90) REVERT: D 10 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.6625 (p90) REVERT: E 13 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6383 (p90) REVERT: F 10 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6606 (p90) REVERT: F 22 GLU cc_start: 0.8357 (tp30) cc_final: 0.8091 (tp30) REVERT: G 13 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6433 (p90) REVERT: H 7 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: H 10 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6684 (p90) REVERT: H 22 GLU cc_start: 0.8405 (tp30) cc_final: 0.8121 (tp30) REVERT: H 36 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8468 (m) REVERT: I 13 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6699 (p90) REVERT: I 19 PHE cc_start: 0.6598 (OUTLIER) cc_final: 0.6168 (p90) REVERT: I 35 MET cc_start: 0.7793 (mmm) cc_final: 0.7522 (mmm) REVERT: J 10 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7300 (p90) REVERT: K 13 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6651 (p90) REVERT: K 19 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.6314 (p90) REVERT: L 10 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7566 (p90) REVERT: M 13 HIS cc_start: 0.6954 (OUTLIER) cc_final: 0.6470 (p90) REVERT: M 34 LEU cc_start: 0.8249 (tp) cc_final: 0.7999 (tp) REVERT: Q 28 LYS cc_start: 0.6171 (mmtt) cc_final: 0.5891 (mmtm) REVERT: Q 35 MET cc_start: 0.7717 (mmm) cc_final: 0.7400 (mmt) REVERT: S 15 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7180 (tm130) REVERT: S 17 LEU cc_start: 0.7515 (tp) cc_final: 0.7277 (tt) REVERT: S 26 SER cc_start: 0.8844 (t) cc_final: 0.8461 (m) REVERT: S 35 MET cc_start: 0.7888 (mmm) cc_final: 0.7558 (mmt) REVERT: T 14 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6544 (t-90) outliers start: 58 outliers final: 32 residues processed: 207 average time/residue: 0.1454 time to fit residues: 39.8999 Evaluate side-chains 227 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 176 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5600 Z= 0.286 Angle : 0.817 7.953 7520 Z= 0.444 Chirality : 0.063 0.246 810 Planarity : 0.003 0.017 990 Dihedral : 10.927 89.742 760 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 10.00 % Allowed : 22.50 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 13 PHE 0.032 0.003 PHE I 19 TYR 0.009 0.001 TYR J 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 177 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7269 (p90) cc_final: 0.6839 (p-80) REVERT: A 19 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.6607 (p90) REVERT: B 10 TYR cc_start: 0.8204 (OUTLIER) cc_final: 0.6628 (p90) REVERT: C 13 HIS cc_start: 0.7142 (p90) cc_final: 0.6768 (p-80) REVERT: C 19 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6446 (p90) REVERT: D 10 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6547 (p90) REVERT: E 13 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6409 (p90) REVERT: F 10 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6756 (p90) REVERT: G 13 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6304 (p90) REVERT: H 10 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.6609 (p90) REVERT: H 22 GLU cc_start: 0.8421 (tp30) cc_final: 0.8117 (tp30) REVERT: H 36 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8401 (m) REVERT: I 13 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6562 (p90) REVERT: J 10 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7332 (p90) REVERT: K 13 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6524 (p90) REVERT: L 10 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7377 (p90) REVERT: M 13 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6339 (p90) REVERT: M 17 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6930 (tp) REVERT: N 35 MET cc_start: 0.7109 (ttm) cc_final: 0.6740 (ttm) REVERT: P 22 GLU cc_start: 0.8229 (tp30) cc_final: 0.8007 (tp30) REVERT: Q 15 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7204 (tm130) REVERT: Q 35 MET cc_start: 0.7654 (mmm) cc_final: 0.7334 (mmt) REVERT: S 15 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7159 (tm130) REVERT: S 26 SER cc_start: 0.8757 (t) cc_final: 0.8368 (m) REVERT: S 35 MET cc_start: 0.7793 (mmm) cc_final: 0.7302 (mmt) REVERT: T 35 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6045 (ttm) outliers start: 56 outliers final: 26 residues processed: 204 average time/residue: 0.1375 time to fit residues: 37.5349 Evaluate side-chains 219 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 175 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 35 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 overall best weight: 1.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5600 Z= 0.351 Angle : 0.882 8.570 7520 Z= 0.476 Chirality : 0.063 0.238 810 Planarity : 0.003 0.016 990 Dihedral : 11.091 87.795 760 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 25.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Rotamer: Outliers : 9.64 % Allowed : 24.11 % Favored : 66.25 % 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: -3.28 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 13 PHE 0.038 0.004 PHE K 19 TYR 0.009 0.001 TYR J 10 ARG 0.002 0.000 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7366 (p90) cc_final: 0.6916 (p-80) REVERT: A 19 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6611 (p90) REVERT: B 10 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.6676 (p90) REVERT: C 13 HIS cc_start: 0.7199 (p90) cc_final: 0.6710 (p90) REVERT: C 19 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6557 (p90) REVERT: D 10 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.6746 (p90) REVERT: E 13 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6392 (p90) REVERT: F 10 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.6873 (p90) REVERT: F 22 GLU cc_start: 0.8435 (tp30) cc_final: 0.8124 (tp30) REVERT: F 36 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8489 (m) REVERT: G 13 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.6388 (p90) REVERT: H 10 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.6563 (p90) REVERT: H 22 GLU cc_start: 0.8405 (tp30) cc_final: 0.8089 (tp30) REVERT: I 13 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6634 (p90) REVERT: J 10 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7420 (p90) REVERT: K 13 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6634 (p90) REVERT: L 10 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7621 (p90) REVERT: M 13 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6365 (p90) REVERT: M 17 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7036 (tp) REVERT: N 35 MET cc_start: 0.7129 (ttm) cc_final: 0.6641 (ttm) REVERT: P 22 GLU cc_start: 0.8336 (tp30) cc_final: 0.8129 (tp30) REVERT: Q 15 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7183 (tm130) REVERT: Q 28 LYS cc_start: 0.5178 (mmtt) cc_final: 0.4812 (mmtm) REVERT: Q 35 MET cc_start: 0.7668 (mmm) cc_final: 0.7421 (mmt) REVERT: S 15 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7224 (tm130) REVERT: S 26 SER cc_start: 0.8817 (t) cc_final: 0.8433 (m) REVERT: S 35 MET cc_start: 0.7838 (mmm) cc_final: 0.7470 (mmt) REVERT: T 35 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6096 (ttm) outliers start: 54 outliers final: 30 residues processed: 193 average time/residue: 0.1461 time to fit residues: 37.6783 Evaluate side-chains 212 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 35 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.0980 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.7218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 5600 Z= 0.475 Angle : 0.985 11.944 7520 Z= 0.531 Chirality : 0.067 0.293 810 Planarity : 0.004 0.018 990 Dihedral : 11.556 89.911 760 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 29.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.96 % Favored : 83.04 % Rotamer: Outliers : 10.00 % Allowed : 24.82 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 13 PHE 0.043 0.004 PHE K 19 TYR 0.010 0.002 TYR E 10 ARG 0.002 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6666 (p90) REVERT: B 10 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.6773 (p90) REVERT: C 19 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6767 (p90) REVERT: D 10 TYR cc_start: 0.8398 (OUTLIER) cc_final: 0.6755 (p90) REVERT: E 13 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6283 (p90) REVERT: F 10 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.6565 (p90) REVERT: F 22 GLU cc_start: 0.8407 (tp30) cc_final: 0.8137 (tp30) REVERT: F 36 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8516 (m) REVERT: G 13 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6303 (p90) REVERT: H 10 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6622 (p90) REVERT: H 22 GLU cc_start: 0.8381 (tp30) cc_final: 0.8107 (tp30) REVERT: I 13 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6798 (p90) REVERT: I 35 MET cc_start: 0.8337 (mmm) cc_final: 0.8051 (mmm) REVERT: J 10 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7499 (p90) REVERT: K 13 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.6849 (p90) REVERT: L 10 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7707 (p90) REVERT: M 13 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6678 (p90) REVERT: M 17 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7038 (tp) REVERT: O 34 LEU cc_start: 0.7650 (tt) cc_final: 0.7318 (tt) REVERT: Q 15 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7195 (tm130) REVERT: Q 35 MET cc_start: 0.7667 (mmm) cc_final: 0.7462 (mmt) REVERT: S 15 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7305 (tm130) REVERT: S 19 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6619 (p90) REVERT: S 26 SER cc_start: 0.8382 (t) cc_final: 0.8030 (m) REVERT: S 35 MET cc_start: 0.7877 (mmm) cc_final: 0.7521 (mmt) REVERT: T 35 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5712 (ttm) outliers start: 56 outliers final: 28 residues processed: 195 average time/residue: 0.1442 time to fit residues: 37.6869 Evaluate side-chains 213 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 166 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 35 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5600 Z= 0.303 Angle : 0.873 10.305 7520 Z= 0.465 Chirality : 0.063 0.257 810 Planarity : 0.003 0.017 990 Dihedral : 11.086 87.364 760 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.80 % Favored : 84.20 % Rotamer: Outliers : 8.04 % Allowed : 25.89 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 13 PHE 0.037 0.003 PHE K 19 TYR 0.010 0.001 TYR J 10 ARG 0.001 0.000 ARG D 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 165 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7237 (p90) cc_final: 0.6802 (p-80) REVERT: A 19 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6540 (p90) REVERT: B 10 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.6628 (p90) REVERT: C 11 GLU cc_start: 0.7460 (mp0) cc_final: 0.7245 (mp0) REVERT: C 13 HIS cc_start: 0.7126 (p90) cc_final: 0.6795 (p-80) REVERT: C 19 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6735 (p90) REVERT: D 10 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.6579 (p90) REVERT: E 13 HIS cc_start: 0.7091 (OUTLIER) cc_final: 0.6460 (p90) REVERT: F 22 GLU cc_start: 0.8402 (tp30) cc_final: 0.8051 (tp30) REVERT: F 36 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8391 (m) REVERT: G 13 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6375 (p90) REVERT: G 15 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7292 (tm-30) REVERT: H 10 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.6668 (p90) REVERT: H 22 GLU cc_start: 0.8386 (tp30) cc_final: 0.8062 (tp30) REVERT: I 13 HIS cc_start: 0.7040 (OUTLIER) cc_final: 0.6553 (p90) REVERT: J 10 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7346 (p90) REVERT: K 13 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6574 (p90) REVERT: L 10 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7481 (p90) REVERT: M 13 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.6407 (p90) REVERT: N 27 ASN cc_start: 0.8499 (t0) cc_final: 0.8231 (t0) REVERT: N 34 LEU cc_start: 0.9034 (tt) cc_final: 0.8793 (tp) REVERT: N 35 MET cc_start: 0.6978 (ttm) cc_final: 0.6440 (ttm) REVERT: O 35 MET cc_start: 0.8201 (mmm) cc_final: 0.7845 (mmm) REVERT: Q 15 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7223 (tm130) REVERT: S 15 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7242 (tm130) REVERT: S 26 SER cc_start: 0.8154 (t) cc_final: 0.7810 (m) REVERT: S 35 MET cc_start: 0.7772 (mmm) cc_final: 0.7258 (mmt) outliers start: 45 outliers final: 23 residues processed: 186 average time/residue: 0.1440 time to fit residues: 35.7477 Evaluate side-chains 197 residues out of total 560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5757 r_free = 0.5757 target = 0.354032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.6080 r_free = 0.6080 target = 0.274836 restraints weight = 8782.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.6127 r_free = 0.6127 target = 0.277518 restraints weight = 4631.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.6163 r_free = 0.6163 target = 0.279261 restraints weight = 2775.157| |-----------------------------------------------------------------------------| r_work (final): 0.5390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.7505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5600 Z= 0.324 Angle : 0.895 10.429 7520 Z= 0.471 Chirality : 0.063 0.214 810 Planarity : 0.003 0.017 990 Dihedral : 11.026 88.466 760 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 7.68 % Allowed : 26.96 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 13 PHE 0.040 0.004 PHE E 19 TYR 0.009 0.001 TYR J 10 ARG 0.002 0.000 ARG D 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1625.72 seconds wall clock time: 30 minutes 9.98 seconds (1809.98 seconds total)