Starting phenix.real_space_refine on Wed Oct 9 21:37:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czp_46424/10_2024/9czp_46424_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czp_46424/10_2024/9czp_46424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czp_46424/10_2024/9czp_46424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czp_46424/10_2024/9czp_46424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czp_46424/10_2024/9czp_46424_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9czp_46424/10_2024/9czp_46424_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 3260 2.51 5 N 840 2.21 5 O 900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 5020 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "E" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "H" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "I" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "J" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "L" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "M" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "N" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "P" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "Q" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "S" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "T" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Time building chain proxies: 4.13, per 1000 atoms: 0.82 Number of scatterers: 5020 At special positions: 0 Unit cell: (91.698, 108.562, 52.7, 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 900 8.00 N 840 7.00 C 3260 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 - 3.00 Amino acid : True - 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: 1.16 Conformation dependent library (CDL) restraints added in 603.7 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.530A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS C 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 12 " --> pdb=" O HIS C 13 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS E 13 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS G 13 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR G 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS I 13 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL G 12 " --> pdb=" O HIS I 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 18 removed outlier: 6.610A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 41 removed outlier: 6.276A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL C 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET A 35 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY C 38 " --> pdb=" O MET A 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY A 37 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL C 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE C 31 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU E 34 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY C 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL E 36 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET C 35 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLY E 38 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY C 37 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL E 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE E 31 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU G 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY E 33 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL G 36 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET E 35 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY G 38 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY E 37 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL G 40 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE G 31 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU I 34 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY G 33 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL I 36 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET G 35 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLY I 38 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY G 37 " --> pdb=" O GLY I 38 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL I 40 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.538A pdb=" N TYR B 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N HIS D 13 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR D 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N HIS F 13 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL D 12 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR F 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N HIS H 13 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 12 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR H 10 " --> pdb=" O GLU J 11 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N HIS J 13 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL H 12 " --> pdb=" O HIS J 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 6.544A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU H 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 41 removed outlier: 6.902A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 36 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL F 36 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU H 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET F 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL H 36 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU J 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET H 35 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL J 36 " --> pdb=" O MET H 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 18 removed outlier: 7.091A pdb=" N GLU M 11 " --> pdb=" O TYR K 10 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL K 12 " --> pdb=" O GLU M 11 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N HIS M 13 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS K 14 " --> pdb=" O HIS M 13 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU O 11 " --> pdb=" O TYR M 10 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL M 12 " --> pdb=" O GLU O 11 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HIS O 13 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS M 14 " --> pdb=" O HIS O 13 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU Q 11 " --> pdb=" O TYR O 10 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL O 12 " --> pdb=" O GLU Q 11 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS Q 13 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS O 14 " --> pdb=" O HIS Q 13 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU S 11 " --> pdb=" O TYR Q 10 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL Q 12 " --> pdb=" O GLU S 11 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS S 13 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS Q 14 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 23 through 27 removed outlier: 6.368A pdb=" N ASP K 23 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER M 26 " --> pdb=" O ASP K 23 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY K 25 " --> pdb=" O SER M 26 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP M 23 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER O 26 " --> pdb=" O ASP M 23 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY M 25 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP O 23 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER Q 26 " --> pdb=" O ASP O 23 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY O 25 " --> pdb=" O SER Q 26 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP Q 23 " --> pdb=" O VAL S 24 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N SER S 26 " --> pdb=" O ASP Q 23 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLY Q 25 " --> pdb=" O SER S 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 30 through 35 removed outlier: 6.902A pdb=" N ILE K 31 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE M 32 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY K 33 " --> pdb=" O ILE M 32 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE M 31 " --> pdb=" O ALA O 30 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE O 32 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY M 33 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE O 31 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE Q 32 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY O 33 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE Q 31 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE S 32 " --> pdb=" O ILE Q 31 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLY Q 33 " --> pdb=" O ILE S 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 39 through 41 removed outlier: 6.339A pdb=" N VAL K 40 " --> pdb=" O ILE M 41 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL M 40 " --> pdb=" O ILE O 41 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL O 40 " --> pdb=" O ILE Q 41 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL Q 40 " --> pdb=" O ILE S 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB4, first strand: chain 'L' and resid 16 through 18 Processing sheet with id=AB5, first strand: chain 'L' and resid 23 through 24 removed outlier: 6.492A pdb=" N ASP L 23 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP N 23 " --> pdb=" O VAL P 24 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP P 23 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP R 23 " --> pdb=" O VAL T 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'L' and resid 30 through 41 removed outlier: 6.589A pdb=" N ALA L 30 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY N 33 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE L 32 " --> pdb=" O GLY N 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET N 35 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU L 34 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLY N 37 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL L 36 " --> pdb=" O GLY N 37 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL N 39 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY L 38 " --> pdb=" O VAL N 39 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE N 41 " --> pdb=" O GLY L 38 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL L 40 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA N 30 " --> pdb=" O ILE P 31 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY P 33 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE N 32 " --> pdb=" O GLY P 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N MET P 35 " --> pdb=" O ILE N 32 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU N 34 " --> pdb=" O MET P 35 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N GLY P 37 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL N 36 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL P 39 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY N 38 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE P 41 " --> pdb=" O GLY N 38 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL N 40 " --> pdb=" O ILE P 41 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA P 30 " --> pdb=" O ILE R 31 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY R 33 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE P 32 " --> pdb=" O GLY R 33 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET R 35 " --> pdb=" O ILE P 32 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU P 34 " --> pdb=" O MET R 35 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLY R 37 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL P 36 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL R 39 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY P 38 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE R 41 " --> pdb=" O GLY P 38 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL P 40 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA R 30 " --> pdb=" O ILE T 31 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY T 33 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N ILE R 32 " --> pdb=" O GLY T 33 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N MET T 35 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N LEU R 34 " --> pdb=" O MET T 35 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N GLY T 37 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL R 36 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL T 39 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY R 38 " --> pdb=" O VAL T 39 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE T 41 " --> pdb=" O GLY R 38 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL R 40 " --> pdb=" O ILE T 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 80 hydrogen bonds defined for protein. 240 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: 1.80 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1358 1.32 - 1.44: 978 1.44 - 1.57: 2719 1.57 - 1.69: 10 1.69 - 1.82: 35 Bond restraints: 5100 Sorted by residual: bond pdb=" C TYR K 10 " pdb=" N GLU K 11 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.38e-02 5.25e+03 2.28e+01 bond pdb=" C TYR O 10 " pdb=" N GLU O 11 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.38e-02 5.25e+03 2.26e+01 bond pdb=" C TYR Q 10 " pdb=" N GLU Q 11 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.38e-02 5.25e+03 2.26e+01 bond pdb=" C TYR S 10 " pdb=" N GLU S 11 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.38e-02 5.25e+03 2.25e+01 bond pdb=" C TYR M 10 " pdb=" N GLU M 11 " ideal model delta sigma weight residual 1.331 1.396 -0.065 1.38e-02 5.25e+03 2.19e+01 ... (remaining 5095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 5612 2.34 - 4.69: 1003 4.69 - 7.03: 184 7.03 - 9.37: 41 9.37 - 11.72: 20 Bond angle restraints: 6860 Sorted by residual: angle pdb=" N VAL H 36 " pdb=" CA VAL H 36 " pdb=" C VAL H 36 " ideal model delta sigma weight residual 110.82 100.97 9.85 9.70e-01 1.06e+00 1.03e+02 angle pdb=" N VAL F 36 " pdb=" CA VAL F 36 " pdb=" C VAL F 36 " ideal model delta sigma weight residual 110.82 100.98 9.84 9.70e-01 1.06e+00 1.03e+02 angle pdb=" N VAL B 36 " pdb=" CA VAL B 36 " pdb=" C VAL B 36 " ideal model delta sigma weight residual 110.82 101.01 9.81 9.70e-01 1.06e+00 1.02e+02 angle pdb=" N VAL J 36 " pdb=" CA VAL J 36 " pdb=" C VAL J 36 " ideal model delta sigma weight residual 110.82 101.01 9.81 9.70e-01 1.06e+00 1.02e+02 angle pdb=" N VAL D 36 " pdb=" CA VAL D 36 " pdb=" C VAL D 36 " ideal model delta sigma weight residual 110.82 101.02 9.80 9.70e-01 1.06e+00 1.02e+02 ... (remaining 6855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.60: 2680 13.60 - 27.19: 85 27.19 - 40.78: 45 40.78 - 54.37: 20 54.37 - 67.97: 10 Dihedral angle restraints: 2840 sinusoidal: 1040 harmonic: 1800 Sorted by residual: dihedral pdb=" CA ASP D 23 " pdb=" CB ASP D 23 " pdb=" CG ASP D 23 " pdb=" OD1 ASP D 23 " ideal model delta sinusoidal sigma weight residual -30.00 -80.93 50.93 1 2.00e+01 2.50e-03 8.87e+00 dihedral pdb=" CA ASP B 23 " pdb=" CB ASP B 23 " pdb=" CG ASP B 23 " pdb=" OD1 ASP B 23 " ideal model delta sinusoidal sigma weight residual -30.00 -80.90 50.90 1 2.00e+01 2.50e-03 8.86e+00 dihedral pdb=" CA ASP H 23 " pdb=" CB ASP H 23 " pdb=" CG ASP H 23 " pdb=" OD1 ASP H 23 " ideal model delta sinusoidal sigma weight residual -30.00 -80.84 50.84 1 2.00e+01 2.50e-03 8.84e+00 ... (remaining 2837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 384 0.075 - 0.150: 249 0.150 - 0.226: 109 0.226 - 0.301: 33 0.301 - 0.376: 5 Chirality restraints: 780 Sorted by residual: 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 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 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 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA HIS H 13 " pdb=" N HIS H 13 " pdb=" C HIS H 13 " pdb=" CB HIS H 13 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 777 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 42 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C ALA Q 42 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA Q 42 " -0.033 2.00e-02 2.50e+03 pdb=" OXT ALA Q 42 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 42 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C ALA M 42 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA M 42 " -0.033 2.00e-02 2.50e+03 pdb=" OXT ALA M 42 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 42 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C ALA K 42 " 0.091 2.00e-02 2.50e+03 pdb=" O ALA K 42 " -0.033 2.00e-02 2.50e+03 pdb=" OXT ALA K 42 " -0.032 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1996 2.90 - 3.40: 4130 3.40 - 3.90: 9200 3.90 - 4.40: 9524 4.40 - 4.90: 18942 Nonbonded interactions: 43792 Sorted by model distance: nonbonded pdb=" NZ LYS I 16 " pdb=" OE1 GLU I 22 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS A 16 " pdb=" OE1 GLU A 22 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS G 16 " pdb=" OE1 GLU G 22 " model vdw 2.402 3.120 nonbonded pdb=" NZ LYS E 16 " pdb=" OE1 GLU E 22 " model vdw 2.403 3.120 nonbonded pdb=" NZ LYS C 16 " pdb=" OE1 GLU C 22 " model vdw 2.403 3.120 ... (remaining 43787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.780 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.021 0.112 5100 Z= 1.418 Angle : 2.005 11.715 6860 Z= 1.329 Chirality : 0.115 0.376 780 Planarity : 0.010 0.053 880 Dihedral : 10.683 67.968 1720 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.21 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS J 14 PHE 0.012 0.003 PHE R 19 TYR 0.013 0.004 TYR Q 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.514 Fit side-chains REVERT: J 10 TYR cc_start: 0.8623 (m-80) cc_final: 0.8384 (m-80) REVERT: M 23 ASP cc_start: 0.7408 (m-30) cc_final: 0.7140 (m-30) REVERT: R 10 TYR cc_start: 0.9011 (m-80) cc_final: 0.8747 (m-10) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1755 time to fit residues: 29.1918 Evaluate side-chains 91 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 27 ASN D 14 HIS F 14 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN H 14 HIS ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS K 14 HIS M 14 HIS O 14 HIS ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 HIS ** Q 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5100 Z= 0.231 Angle : 0.562 7.497 6860 Z= 0.324 Chirality : 0.058 0.136 780 Planarity : 0.002 0.011 880 Dihedral : 7.169 48.199 700 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.80 % Allowed : 7.80 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.51 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 14 PHE 0.007 0.001 PHE A 20 TYR 0.015 0.002 TYR R 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.532 Fit side-chains REVERT: B 15 GLN cc_start: 0.8997 (mp10) cc_final: 0.8425 (mp10) REVERT: F 15 GLN cc_start: 0.9186 (mp10) cc_final: 0.8575 (mp10) REVERT: H 10 TYR cc_start: 0.8650 (m-80) cc_final: 0.8059 (m-80) REVERT: K 23 ASP cc_start: 0.7565 (m-30) cc_final: 0.7280 (m-30) REVERT: M 15 GLN cc_start: 0.8798 (mp10) cc_final: 0.8412 (mp10) REVERT: R 10 TYR cc_start: 0.8580 (m-80) cc_final: 0.8283 (m-10) REVERT: T 10 TYR cc_start: 0.8445 (m-80) cc_final: 0.7984 (m-80) outliers start: 4 outliers final: 4 residues processed: 134 average time/residue: 0.1418 time to fit residues: 25.4390 Evaluate side-chains 119 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain N residue 15 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 5100 Z= 0.458 Angle : 0.646 6.843 6860 Z= 0.364 Chirality : 0.061 0.138 780 Planarity : 0.002 0.013 880 Dihedral : 6.704 40.153 700 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.00 % Allowed : 10.00 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.31), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 14 PHE 0.010 0.001 PHE I 19 TYR 0.021 0.003 TYR Q 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.562 Fit side-chains REVERT: D 16 LYS cc_start: 0.9136 (tttt) cc_final: 0.8835 (tttp) REVERT: H 10 TYR cc_start: 0.8659 (m-80) cc_final: 0.8177 (m-80) REVERT: M 15 GLN cc_start: 0.9012 (mp10) cc_final: 0.8599 (mp10) REVERT: O 15 GLN cc_start: 0.8970 (mp10) cc_final: 0.8712 (mp10) REVERT: Q 10 TYR cc_start: 0.6936 (m-80) cc_final: 0.6722 (m-80) REVERT: R 10 TYR cc_start: 0.8871 (m-80) cc_final: 0.8605 (m-10) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 0.1283 time to fit residues: 20.8032 Evaluate side-chains 115 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.3980 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 0.0060 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5100 Z= 0.181 Angle : 0.506 7.647 6860 Z= 0.281 Chirality : 0.056 0.144 780 Planarity : 0.002 0.011 880 Dihedral : 5.747 31.820 700 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.20 % Allowed : 11.80 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 14 PHE 0.007 0.000 PHE A 20 TYR 0.009 0.001 TYR Q 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 125 time to evaluate : 1.763 Fit side-chains REVERT: B 15 GLN cc_start: 0.8960 (mp10) cc_final: 0.8173 (mp10) REVERT: D 16 LYS cc_start: 0.9052 (tttt) cc_final: 0.8793 (tttp) REVERT: F 15 GLN cc_start: 0.9147 (mp10) cc_final: 0.8287 (mp10) REVERT: H 10 TYR cc_start: 0.8550 (m-80) cc_final: 0.8184 (m-80) REVERT: I 28 LYS cc_start: 0.8109 (mttp) cc_final: 0.7870 (mmmt) REVERT: M 15 GLN cc_start: 0.8866 (mp10) cc_final: 0.8459 (mp10) REVERT: O 15 GLN cc_start: 0.8903 (mp10) cc_final: 0.8694 (mp10) REVERT: S 15 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7469 (mp10) outliers start: 11 outliers final: 8 residues processed: 130 average time/residue: 0.1614 time to fit residues: 28.7424 Evaluate side-chains 128 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN E 27 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5100 Z= 0.360 Angle : 0.584 7.062 6860 Z= 0.326 Chirality : 0.058 0.142 780 Planarity : 0.002 0.012 880 Dihedral : 5.803 31.840 700 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.60 % Allowed : 13.40 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.84 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 14 PHE 0.007 0.001 PHE J 19 TYR 0.014 0.002 TYR P 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.641 Fit side-chains REVERT: B 15 GLN cc_start: 0.9051 (mp10) cc_final: 0.8193 (mp10) REVERT: D 16 LYS cc_start: 0.9123 (tttt) cc_final: 0.8906 (tttp) REVERT: H 10 TYR cc_start: 0.8615 (m-80) cc_final: 0.8197 (m-80) REVERT: I 28 LYS cc_start: 0.8133 (mttp) cc_final: 0.7918 (mmmt) REVERT: K 10 TYR cc_start: 0.6765 (m-80) cc_final: 0.5081 (p90) REVERT: M 15 GLN cc_start: 0.8941 (mp10) cc_final: 0.8572 (mp10) REVERT: O 15 GLN cc_start: 0.8924 (mp10) cc_final: 0.8691 (mp10) REVERT: P 15 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8848 (pm20) REVERT: Q 15 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: R 10 TYR cc_start: 0.8732 (m-80) cc_final: 0.8282 (m-10) REVERT: S 15 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7477 (mp10) outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 0.1387 time to fit residues: 23.9186 Evaluate side-chains 125 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 5100 Z= 0.496 Angle : 0.652 7.744 6860 Z= 0.364 Chirality : 0.060 0.141 780 Planarity : 0.002 0.012 880 Dihedral : 6.065 34.248 700 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.00 % Allowed : 14.00 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 14 PHE 0.008 0.001 PHE N 19 TYR 0.015 0.002 TYR R 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.703 Fit side-chains REVERT: B 10 TYR cc_start: 0.8160 (m-80) cc_final: 0.7868 (m-80) REVERT: D 16 LYS cc_start: 0.9160 (tttt) cc_final: 0.8932 (tttp) REVERT: H 10 TYR cc_start: 0.8694 (m-80) cc_final: 0.8272 (m-80) REVERT: I 28 LYS cc_start: 0.8218 (mttp) cc_final: 0.7934 (mmmt) REVERT: M 15 GLN cc_start: 0.8956 (mp10) cc_final: 0.8567 (mp10) REVERT: Q 15 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: S 15 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7474 (mp10) outliers start: 15 outliers final: 11 residues processed: 118 average time/residue: 0.1453 time to fit residues: 23.4984 Evaluate side-chains 120 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 27 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5100 Z= 0.174 Angle : 0.511 7.758 6860 Z= 0.282 Chirality : 0.056 0.147 780 Planarity : 0.002 0.010 880 Dihedral : 5.353 30.001 700 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.60 % Allowed : 14.60 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 14 PHE 0.007 0.001 PHE G 20 TYR 0.011 0.001 TYR M 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.601 Fit side-chains REVERT: B 15 GLN cc_start: 0.9013 (mp10) cc_final: 0.8191 (mp10) REVERT: D 16 LYS cc_start: 0.9097 (tttt) cc_final: 0.8767 (tttp) REVERT: H 10 TYR cc_start: 0.8564 (m-80) cc_final: 0.8287 (m-80) REVERT: I 28 LYS cc_start: 0.8159 (mttp) cc_final: 0.7904 (mmmt) REVERT: M 15 GLN cc_start: 0.8856 (mp10) cc_final: 0.8517 (mp10) REVERT: O 15 GLN cc_start: 0.8778 (mp10) cc_final: 0.8439 (mp10) REVERT: Q 15 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: S 15 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7324 (mp10) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 0.1295 time to fit residues: 21.7401 Evaluate side-chains 124 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 5100 Z= 0.462 Angle : 0.644 8.153 6860 Z= 0.356 Chirality : 0.059 0.146 780 Planarity : 0.002 0.011 880 Dihedral : 5.808 31.637 700 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.40 % Allowed : 14.60 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 14 PHE 0.007 0.001 PHE J 19 TYR 0.016 0.002 TYR P 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.596 Fit side-chains REVERT: D 16 LYS cc_start: 0.9121 (tttt) cc_final: 0.8797 (tttp) REVERT: H 10 TYR cc_start: 0.8696 (m-80) cc_final: 0.8298 (m-80) REVERT: I 28 LYS cc_start: 0.8199 (mttp) cc_final: 0.7939 (mmmt) REVERT: Q 10 TYR cc_start: 0.7493 (m-80) cc_final: 0.7246 (m-80) REVERT: Q 15 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7665 (mp10) REVERT: S 15 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7472 (mp10) outliers start: 17 outliers final: 12 residues processed: 112 average time/residue: 0.1314 time to fit residues: 20.1908 Evaluate side-chains 117 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5100 Z= 0.223 Angle : 0.539 8.591 6860 Z= 0.296 Chirality : 0.057 0.139 780 Planarity : 0.002 0.010 880 Dihedral : 5.348 30.129 700 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.40 % Allowed : 15.60 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Q 13 PHE 0.004 0.001 PHE G 20 TYR 0.010 0.001 TYR D 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.618 Fit side-chains REVERT: B 15 GLN cc_start: 0.9049 (mp10) cc_final: 0.8207 (mp10) REVERT: D 16 LYS cc_start: 0.9087 (tttt) cc_final: 0.8830 (tttp) REVERT: H 10 TYR cc_start: 0.8607 (m-80) cc_final: 0.8349 (m-80) REVERT: I 28 LYS cc_start: 0.8173 (mttp) cc_final: 0.7923 (mmmt) REVERT: M 15 GLN cc_start: 0.8915 (mp10) cc_final: 0.8538 (mp10) REVERT: O 15 GLN cc_start: 0.8834 (mp10) cc_final: 0.8467 (mp10) REVERT: Q 15 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: S 15 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7480 (mp10) outliers start: 12 outliers final: 9 residues processed: 120 average time/residue: 0.1406 time to fit residues: 23.0386 Evaluate side-chains 127 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 5100 Z= 0.397 Angle : 0.613 8.707 6860 Z= 0.338 Chirality : 0.058 0.142 780 Planarity : 0.002 0.011 880 Dihedral : 5.597 30.485 700 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 3.20 % Allowed : 14.60 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.32), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 13 PHE 0.008 0.001 PHE J 19 TYR 0.014 0.002 TYR D 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.585 Fit side-chains REVERT: D 16 LYS cc_start: 0.9130 (tttt) cc_final: 0.8867 (tttp) REVERT: H 10 TYR cc_start: 0.8684 (m-80) cc_final: 0.8348 (m-80) REVERT: M 15 GLN cc_start: 0.9002 (mp10) cc_final: 0.8622 (mp10) REVERT: Q 15 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: S 15 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7485 (mp10) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 0.1343 time to fit residues: 22.4352 Evaluate side-chains 122 residues out of total 500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 35 MET Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain L residue 15 GLN Chi-restraints excluded: chain N residue 15 GLN Chi-restraints excluded: chain O residue 10 TYR Chi-restraints excluded: chain O residue 35 MET Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain Q residue 15 GLN Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 26 SER Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain T residue 15 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.115536 restraints weight = 6775.144| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.52 r_work: 0.3598 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5100 Z= 0.140 Angle : 0.514 8.466 6860 Z= 0.279 Chirality : 0.056 0.135 780 Planarity : 0.002 0.010 880 Dihedral : 5.005 28.267 700 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.80 % Allowed : 15.40 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.33), residues: 640 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 14 PHE 0.004 0.000 PHE G 20 TYR 0.010 0.001 TYR N 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.29 seconds wall clock time: 29 minutes 53.86 seconds (1793.86 seconds total)