Starting phenix.real_space_refine on Tue Feb 13 16:50:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adv_15371/02_2024/8adv_15371.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adv_15371/02_2024/8adv_15371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adv_15371/02_2024/8adv_15371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adv_15371/02_2024/8adv_15371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adv_15371/02_2024/8adv_15371.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8adv_15371/02_2024/8adv_15371.pdb" } resolution = 2.98 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= 0.002 sd= 0.013 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 4320 2.51 5 N 1200 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6920 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "B" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "C" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "D" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "E" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "F" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "G" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "H" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "I" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "J" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Time building chain proxies: 3.95, per 1000 atoms: 0.57 Number of scatterers: 6920 At special positions: 0 Unit cell: (120.75, 129.15, 51.45, 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 1380 8.00 N 1200 7.00 C 4320 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: 2.18 Conformation dependent library (CDL) restraints added in 1.5 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 20 removed outlier: 6.280A pdb=" N VAL A 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA C 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU C 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA A 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA E 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA C 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU E 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL E 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA G 18 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA E 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU G 20 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA E 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL G 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA I 18 " --> pdb=" O VAL G 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA G 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU I 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 35 removed outlier: 6.764A pdb=" N LYS C 34 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU A 35 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS E 34 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 35 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS G 34 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU E 35 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS I 34 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU G 35 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.303A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR E 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR G 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 58 removed outlier: 9.280A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N VAL C 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS E 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU C 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL E 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL G 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY E 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR G 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL E 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS G 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU E 57 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL G 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL I 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY G 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR I 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N LYS I 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU G 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=AA9, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AB1, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AB2, first strand: chain 'A' and resid 82 through 83 removed outlier: 5.969A pdb=" N VAL A 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL C 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL E 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL G 82 " --> pdb=" O GLU I 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.804A pdb=" N GLY A 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS C 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY C 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS E 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY E 93 " --> pdb=" O PHE G 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS G 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 95 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY G 93 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS I 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL G 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 8 through 9 Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 20 removed outlier: 6.279A pdb=" N VAL B 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA D 18 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU D 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 15 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA F 18 " --> pdb=" O VAL D 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA D 17 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLU F 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA D 19 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL F 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA H 18 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA F 17 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU H 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA F 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL H 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ALA J 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA H 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLU J 20 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA H 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 35 removed outlier: 6.764A pdb=" N LYS D 34 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU B 35 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS F 34 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU D 35 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS H 34 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU F 35 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS J 34 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU H 35 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.303A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR F 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR H 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 58 removed outlier: 9.279A pdb=" N VAL B 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL D 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY B 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR D 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS D 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU B 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL D 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N THR F 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL D 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N LYS F 58 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU D 57 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL F 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N VAL H 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N GLY F 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR H 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N VAL F 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS H 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU F 57 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 9.279A pdb=" N VAL H 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N VAL J 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLY H 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N THR J 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA H 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ALA J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N VAL H 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N LYS J 58 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU H 57 " --> pdb=" O LYS J 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AC3, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AC4, first strand: chain 'B' and resid 75 through 79 Processing sheet with id=AC5, first strand: chain 'B' and resid 82 through 83 removed outlier: 5.968A pdb=" N VAL B 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL D 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL F 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL H 82 " --> pdb=" O GLU J 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.804A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY D 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS F 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY F 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LYS H 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL F 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY H 93 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS J 96 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL H 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 144 hydrogen bonds defined for protein. 432 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: 1.69 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2290 1.34 - 1.45: 656 1.45 - 1.57: 3964 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 6950 Sorted by residual: bond pdb=" CG LEU E 38 " pdb=" CD1 LEU E 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG LEU D 38 " pdb=" CD1 LEU D 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 bond pdb=" CG LEU G 38 " pdb=" CD1 LEU G 38 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.72e+00 ... (remaining 6945 not shown) Histogram of bond angle deviations from ideal: 100.47 - 106.61: 72 106.61 - 112.74: 4168 112.74 - 118.88: 1672 118.88 - 125.01: 3398 125.01 - 131.14: 10 Bond angle restraints: 9320 Sorted by residual: angle pdb=" C VAL J 3 " pdb=" N PHE J 4 " pdb=" CA PHE J 4 " ideal model delta sigma weight residual 122.53 118.59 3.94 1.61e+00 3.86e-01 6.00e+00 angle pdb=" C VAL C 3 " pdb=" N PHE C 4 " pdb=" CA PHE C 4 " ideal model delta sigma weight residual 122.53 118.59 3.94 1.61e+00 3.86e-01 6.00e+00 angle pdb=" C VAL D 3 " pdb=" N PHE D 4 " pdb=" CA PHE D 4 " ideal model delta sigma weight residual 122.53 118.59 3.94 1.61e+00 3.86e-01 5.99e+00 angle pdb=" C VAL E 3 " pdb=" N PHE E 4 " pdb=" CA PHE E 4 " ideal model delta sigma weight residual 122.53 118.59 3.94 1.61e+00 3.86e-01 5.99e+00 angle pdb=" C VAL B 3 " pdb=" N PHE B 4 " pdb=" CA PHE B 4 " ideal model delta sigma weight residual 122.53 118.60 3.93 1.61e+00 3.86e-01 5.97e+00 ... (remaining 9315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 3880 15.24 - 30.48: 190 30.48 - 45.72: 70 45.72 - 60.96: 30 60.96 - 76.20: 10 Dihedral angle restraints: 4180 sinusoidal: 1490 harmonic: 2690 Sorted by residual: dihedral pdb=" CA ALA B 85 " pdb=" C ALA B 85 " pdb=" N GLY B 86 " pdb=" CA GLY B 86 " ideal model delta harmonic sigma weight residual 180.00 163.14 16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ALA E 85 " pdb=" C ALA E 85 " pdb=" N GLY E 86 " pdb=" CA GLY E 86 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ALA J 85 " pdb=" C ALA J 85 " pdb=" N GLY J 86 " pdb=" CA GLY J 86 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 4177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 578 0.033 - 0.066: 339 0.066 - 0.099: 168 0.099 - 0.132: 65 0.132 - 0.165: 10 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CB VAL C 37 " pdb=" CA VAL C 37 " pdb=" CG1 VAL C 37 " pdb=" CG2 VAL C 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CB VAL B 37 " pdb=" CA VAL B 37 " pdb=" CG1 VAL B 37 " pdb=" CG2 VAL B 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CB VAL F 37 " pdb=" CA VAL F 37 " pdb=" CG1 VAL F 37 " pdb=" CG2 VAL F 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 1157 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 4 " -0.011 2.00e-02 2.50e+03 8.78e-03 1.35e+00 pdb=" CG PHE G 4 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE G 4 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE G 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE G 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE G 4 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.011 2.00e-02 2.50e+03 8.71e-03 1.33e+00 pdb=" CG PHE A 4 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 4 " 0.011 2.00e-02 2.50e+03 8.64e-03 1.31e+00 pdb=" CG PHE F 4 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE F 4 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 4 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 4 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 4 " 0.003 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 184 2.68 - 3.24: 6273 3.24 - 3.79: 10911 3.79 - 4.35: 15601 4.35 - 4.90: 27802 Nonbonded interactions: 60771 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE2 GLU C 46 " model vdw 2.127 2.440 nonbonded pdb=" OH TYR E 39 " pdb=" OE2 GLU E 46 " model vdw 2.127 2.440 nonbonded pdb=" OH TYR F 39 " pdb=" OE2 GLU F 46 " model vdw 2.127 2.440 nonbonded pdb=" OH TYR I 39 " pdb=" OE2 GLU I 46 " model vdw 2.128 2.440 nonbonded pdb=" OH TYR D 39 " pdb=" OE2 GLU D 46 " model vdw 2.128 2.440 ... (remaining 60766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.660 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: 3.500 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.470 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.006 0.064 6950 Z= 0.378 Angle : 0.636 4.991 9320 Z= 0.365 Chirality : 0.053 0.165 1160 Planarity : 0.002 0.009 1170 Dihedral : 12.650 76.203 2480 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 1.45 % Allowed : 0.00 % Favored : 98.55 % 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: -3.72 (0.21), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 50 PHE 0.020 0.005 PHE G 4 TYR 0.015 0.004 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 0.808 Fit side-chains REVERT: A 5 MET cc_start: 0.7766 (ttm) cc_final: 0.7468 (ttm) REVERT: B 65 ASN cc_start: 0.8795 (m110) cc_final: 0.8525 (m110) REVERT: C 61 GLU cc_start: 0.7573 (mp0) cc_final: 0.7114 (mp0) REVERT: E 5 MET cc_start: 0.7884 (ttm) cc_final: 0.7680 (ttm) REVERT: E 65 ASN cc_start: 0.8599 (m110) cc_final: 0.8387 (m-40) REVERT: G 61 GLU cc_start: 0.7429 (mp0) cc_final: 0.7210 (mp0) REVERT: I 2 ASP cc_start: 0.8041 (m-30) cc_final: 0.7718 (m-30) REVERT: I 65 ASN cc_start: 0.8531 (m110) cc_final: 0.8251 (m-40) REVERT: J 65 ASN cc_start: 0.8568 (m110) cc_final: 0.8077 (m110) outliers start: 10 outliers final: 0 residues processed: 157 average time/residue: 1.2086 time to fit residues: 199.1809 Evaluate side-chains 149 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 99 GLN I 99 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.036 6950 Z= 0.544 Angle : 0.667 6.795 9320 Z= 0.369 Chirality : 0.054 0.131 1160 Planarity : 0.003 0.011 1170 Dihedral : 5.689 20.481 990 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 5.22 % Allowed : 11.88 % Favored : 82.90 % 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: -3.76 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.16), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.022 0.005 PHE C 4 TYR 0.026 0.007 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 0.796 Fit side-chains REVERT: A 5 MET cc_start: 0.7733 (ttm) cc_final: 0.7428 (ttm) REVERT: B 65 ASN cc_start: 0.8773 (m110) cc_final: 0.8503 (m110) REVERT: E 5 MET cc_start: 0.7962 (ttm) cc_final: 0.7743 (ttm) REVERT: E 65 ASN cc_start: 0.8681 (m110) cc_final: 0.8454 (m-40) REVERT: G 61 GLU cc_start: 0.7683 (mp0) cc_final: 0.7330 (mp0) REVERT: H 2 ASP cc_start: 0.8044 (m-30) cc_final: 0.7693 (m-30) REVERT: H 20 GLU cc_start: 0.8049 (tt0) cc_final: 0.7788 (tt0) REVERT: I 65 ASN cc_start: 0.8521 (m110) cc_final: 0.8233 (m-40) REVERT: J 65 ASN cc_start: 0.8560 (m110) cc_final: 0.8090 (m110) outliers start: 36 outliers final: 24 residues processed: 184 average time/residue: 1.1646 time to fit residues: 225.3228 Evaluate side-chains 193 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN F 99 GLN I 99 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 6950 Z= 0.303 Angle : 0.548 6.046 9320 Z= 0.304 Chirality : 0.050 0.123 1160 Planarity : 0.002 0.008 1170 Dihedral : 5.304 17.836 990 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.22 % Allowed : 15.94 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.018 0.004 PHE C 4 TYR 0.015 0.004 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 0.846 Fit side-chains REVERT: A 5 MET cc_start: 0.7558 (ttm) cc_final: 0.7235 (ttm) REVERT: B 65 ASN cc_start: 0.8750 (m110) cc_final: 0.8479 (m110) REVERT: E 65 ASN cc_start: 0.8670 (m110) cc_final: 0.8432 (m-40) REVERT: G 20 GLU cc_start: 0.7894 (tt0) cc_final: 0.7640 (tm-30) REVERT: G 61 GLU cc_start: 0.7645 (mp0) cc_final: 0.7167 (mp0) REVERT: I 61 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: I 65 ASN cc_start: 0.8505 (m110) cc_final: 0.8224 (m-40) REVERT: J 65 ASN cc_start: 0.8554 (m110) cc_final: 0.8095 (m110) outliers start: 36 outliers final: 21 residues processed: 174 average time/residue: 1.1494 time to fit residues: 210.4759 Evaluate side-chains 183 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.029 6950 Z= 0.467 Angle : 0.614 6.108 9320 Z= 0.340 Chirality : 0.052 0.128 1160 Planarity : 0.002 0.009 1170 Dihedral : 5.508 20.179 990 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 7.39 % Allowed : 16.09 % Favored : 76.52 % 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: -3.68 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.019 0.005 PHE A 4 TYR 0.020 0.005 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 168 time to evaluate : 0.864 Fit side-chains REVERT: A 5 MET cc_start: 0.7590 (ttm) cc_final: 0.7276 (ttm) REVERT: A 65 ASN cc_start: 0.8911 (m110) cc_final: 0.8612 (m110) REVERT: C 2 ASP cc_start: 0.7792 (m-30) cc_final: 0.7507 (m-30) REVERT: E 65 ASN cc_start: 0.8660 (m110) cc_final: 0.8417 (m-40) REVERT: G 20 GLU cc_start: 0.7912 (tt0) cc_final: 0.7639 (tm-30) REVERT: G 61 GLU cc_start: 0.7610 (mp0) cc_final: 0.7235 (mp0) REVERT: H 2 ASP cc_start: 0.8071 (m-30) cc_final: 0.7673 (m-30) REVERT: H 20 GLU cc_start: 0.8015 (tt0) cc_final: 0.7752 (tt0) REVERT: H 61 GLU cc_start: 0.7887 (mp0) cc_final: 0.7471 (mp0) REVERT: I 2 ASP cc_start: 0.8091 (m-30) cc_final: 0.7776 (m-30) REVERT: I 65 ASN cc_start: 0.8527 (m110) cc_final: 0.8269 (m-40) REVERT: J 61 GLU cc_start: 0.8087 (mp0) cc_final: 0.7885 (mp0) REVERT: J 65 ASN cc_start: 0.8572 (m110) cc_final: 0.8110 (m110) outliers start: 51 outliers final: 40 residues processed: 187 average time/residue: 1.1297 time to fit residues: 222.5753 Evaluate side-chains 207 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 chunk 60 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 6950 Z= 0.272 Angle : 0.527 5.264 9320 Z= 0.292 Chirality : 0.050 0.123 1160 Planarity : 0.002 0.008 1170 Dihedral : 5.183 17.431 990 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 6.38 % Allowed : 17.54 % Favored : 76.09 % 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: -3.66 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.017 0.004 PHE H 4 TYR 0.014 0.003 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 0.696 Fit side-chains REVERT: A 5 MET cc_start: 0.7532 (ttm) cc_final: 0.7234 (ttm) REVERT: A 65 ASN cc_start: 0.8912 (m110) cc_final: 0.8626 (m110) REVERT: B 5 MET cc_start: 0.7796 (ttm) cc_final: 0.7462 (ttm) REVERT: C 2 ASP cc_start: 0.7713 (m-30) cc_final: 0.7433 (m-30) REVERT: C 20 GLU cc_start: 0.7797 (tt0) cc_final: 0.7380 (tt0) REVERT: D 1 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6325 (ttt) REVERT: E 65 ASN cc_start: 0.8658 (m110) cc_final: 0.8392 (m-40) REVERT: G 20 GLU cc_start: 0.7896 (tt0) cc_final: 0.7598 (tm-30) REVERT: G 35 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6773 (tp30) REVERT: G 61 GLU cc_start: 0.7519 (mp0) cc_final: 0.7245 (mp0) REVERT: H 20 GLU cc_start: 0.7971 (tt0) cc_final: 0.7714 (tt0) REVERT: H 61 GLU cc_start: 0.7801 (mp0) cc_final: 0.7406 (mp0) REVERT: I 61 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: I 65 ASN cc_start: 0.8597 (m110) cc_final: 0.8341 (m-40) REVERT: J 61 GLU cc_start: 0.8106 (mp0) cc_final: 0.7903 (mp0) REVERT: J 65 ASN cc_start: 0.8571 (m110) cc_final: 0.8035 (m110) outliers start: 44 outliers final: 33 residues processed: 181 average time/residue: 1.1519 time to fit residues: 219.0044 Evaluate side-chains 197 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.038 6950 Z= 0.644 Angle : 0.686 6.450 9320 Z= 0.378 Chirality : 0.055 0.147 1160 Planarity : 0.003 0.016 1170 Dihedral : 5.729 22.215 990 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 7.83 % Allowed : 17.54 % Favored : 74.64 % 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: -3.68 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.023 0.005 PHE A 4 TYR 0.021 0.005 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 164 time to evaluate : 0.926 Fit side-chains REVERT: A 5 MET cc_start: 0.7715 (ttm) cc_final: 0.7408 (ttm) REVERT: A 65 ASN cc_start: 0.8899 (m110) cc_final: 0.8611 (m110) REVERT: C 2 ASP cc_start: 0.7780 (m-30) cc_final: 0.7506 (m-30) REVERT: E 65 ASN cc_start: 0.8663 (m110) cc_final: 0.8287 (m110) REVERT: G 35 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6896 (tp30) REVERT: G 61 GLU cc_start: 0.7639 (mp0) cc_final: 0.7369 (mp0) REVERT: H 2 ASP cc_start: 0.8191 (m-30) cc_final: 0.7758 (m-30) REVERT: H 20 GLU cc_start: 0.8041 (tt0) cc_final: 0.7802 (tt0) REVERT: H 61 GLU cc_start: 0.7832 (mp0) cc_final: 0.7173 (mp0) REVERT: I 2 ASP cc_start: 0.8205 (m-30) cc_final: 0.7884 (m-30) REVERT: I 61 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: I 65 ASN cc_start: 0.8623 (m110) cc_final: 0.8376 (m-40) REVERT: J 65 ASN cc_start: 0.8561 (m110) cc_final: 0.8019 (m110) outliers start: 54 outliers final: 42 residues processed: 186 average time/residue: 1.1632 time to fit residues: 227.7846 Evaluate side-chains 208 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6950 Z= 0.202 Angle : 0.510 5.509 9320 Z= 0.282 Chirality : 0.049 0.121 1160 Planarity : 0.002 0.017 1170 Dihedral : 5.136 16.958 990 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 5.94 % Allowed : 20.72 % Favored : 73.33 % 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: -3.69 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 50 PHE 0.018 0.003 PHE H 4 TYR 0.011 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 0.784 Fit side-chains REVERT: A 5 MET cc_start: 0.7533 (ttm) cc_final: 0.7243 (ttm) REVERT: A 65 ASN cc_start: 0.8879 (m110) cc_final: 0.8592 (m110) REVERT: B 5 MET cc_start: 0.7468 (ttp) cc_final: 0.7213 (ttm) REVERT: C 2 ASP cc_start: 0.7692 (m-30) cc_final: 0.7430 (m-30) REVERT: E 65 ASN cc_start: 0.8634 (m110) cc_final: 0.8322 (m-40) REVERT: G 35 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6797 (tp30) REVERT: G 61 GLU cc_start: 0.7484 (mp0) cc_final: 0.7240 (mp0) REVERT: H 2 ASP cc_start: 0.8138 (m-30) cc_final: 0.7612 (m-30) REVERT: H 20 GLU cc_start: 0.8016 (tt0) cc_final: 0.7749 (tt0) REVERT: H 61 GLU cc_start: 0.7744 (mp0) cc_final: 0.7183 (mp0) REVERT: I 2 ASP cc_start: 0.7791 (m-30) cc_final: 0.7530 (m-30) REVERT: I 61 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: I 65 ASN cc_start: 0.8595 (m110) cc_final: 0.8359 (m-40) REVERT: J 65 ASN cc_start: 0.8535 (m110) cc_final: 0.7985 (m110) outliers start: 41 outliers final: 29 residues processed: 184 average time/residue: 1.1974 time to fit residues: 231.6373 Evaluate side-chains 192 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 83 optimal weight: 0.0570 chunk 75 optimal weight: 8.9990 overall best weight: 4.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6950 Z= 0.362 Angle : 0.564 6.082 9320 Z= 0.311 Chirality : 0.050 0.124 1160 Planarity : 0.002 0.018 1170 Dihedral : 5.278 18.837 990 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 5.94 % Allowed : 21.88 % Favored : 72.17 % 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: -3.68 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.017 0.004 PHE H 4 TYR 0.016 0.004 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 0.798 Fit side-chains REVERT: A 5 MET cc_start: 0.7555 (ttm) cc_final: 0.7256 (ttm) REVERT: A 65 ASN cc_start: 0.8864 (m110) cc_final: 0.8583 (m110) REVERT: C 2 ASP cc_start: 0.7735 (m-30) cc_final: 0.7454 (m-30) REVERT: D 1 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6122 (ttt) REVERT: E 65 ASN cc_start: 0.8633 (m110) cc_final: 0.8319 (m-40) REVERT: G 35 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6819 (tp30) REVERT: H 2 ASP cc_start: 0.8148 (m-30) cc_final: 0.7717 (m-30) REVERT: H 20 GLU cc_start: 0.7974 (tt0) cc_final: 0.7716 (tt0) REVERT: H 61 GLU cc_start: 0.7759 (mp0) cc_final: 0.7278 (mp0) REVERT: I 2 ASP cc_start: 0.8058 (m-30) cc_final: 0.7737 (m-30) REVERT: I 61 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: I 65 ASN cc_start: 0.8572 (m110) cc_final: 0.8343 (m-40) REVERT: J 65 ASN cc_start: 0.8540 (m110) cc_final: 0.7993 (m110) outliers start: 41 outliers final: 32 residues processed: 182 average time/residue: 1.1370 time to fit residues: 217.7759 Evaluate side-chains 199 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 6.9990 chunk 83 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 6950 Z= 0.313 Angle : 0.555 5.953 9320 Z= 0.306 Chirality : 0.050 0.123 1160 Planarity : 0.002 0.016 1170 Dihedral : 5.254 18.099 990 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 6.38 % Allowed : 22.03 % Favored : 71.59 % 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: -3.70 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.016 0.004 PHE H 4 TYR 0.014 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 0.821 Fit side-chains REVERT: A 5 MET cc_start: 0.7536 (ttm) cc_final: 0.7241 (ttm) REVERT: A 65 ASN cc_start: 0.8867 (m110) cc_final: 0.8579 (m110) REVERT: C 2 ASP cc_start: 0.7717 (m-30) cc_final: 0.7454 (m-30) REVERT: C 20 GLU cc_start: 0.7824 (tt0) cc_final: 0.7381 (tt0) REVERT: C 79 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: D 1 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6112 (ttt) REVERT: E 65 ASN cc_start: 0.8618 (m110) cc_final: 0.8306 (m-40) REVERT: G 35 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6795 (tp30) REVERT: H 2 ASP cc_start: 0.8151 (m-30) cc_final: 0.7689 (m-30) REVERT: H 20 GLU cc_start: 0.7971 (tt0) cc_final: 0.7713 (tt0) REVERT: H 61 GLU cc_start: 0.7772 (mp0) cc_final: 0.7285 (mp0) REVERT: I 2 ASP cc_start: 0.8032 (m-30) cc_final: 0.7714 (m-30) REVERT: I 65 ASN cc_start: 0.8590 (m110) cc_final: 0.8361 (m-40) REVERT: J 65 ASN cc_start: 0.8529 (m110) cc_final: 0.7981 (m110) outliers start: 44 outliers final: 37 residues processed: 182 average time/residue: 1.1353 time to fit residues: 217.7536 Evaluate side-chains 201 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 161 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 6950 Z= 0.454 Angle : 0.620 6.563 9320 Z= 0.342 Chirality : 0.052 0.128 1160 Planarity : 0.002 0.020 1170 Dihedral : 5.520 20.470 990 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 6.23 % Allowed : 21.88 % Favored : 71.88 % 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: -3.72 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.019 0.005 PHE A 4 TYR 0.018 0.004 TYR E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 162 time to evaluate : 0.813 Fit side-chains REVERT: A 5 MET cc_start: 0.7587 (ttm) cc_final: 0.7285 (ttm) REVERT: A 20 GLU cc_start: 0.7799 (tt0) cc_final: 0.7538 (mm-30) REVERT: C 2 ASP cc_start: 0.7756 (m-30) cc_final: 0.7473 (m-30) REVERT: C 20 GLU cc_start: 0.7797 (tt0) cc_final: 0.7282 (tt0) REVERT: C 79 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: D 1 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.6197 (ttt) REVERT: E 65 ASN cc_start: 0.8626 (m110) cc_final: 0.8256 (m110) REVERT: G 35 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: H 2 ASP cc_start: 0.8195 (m-30) cc_final: 0.7773 (m-30) REVERT: H 20 GLU cc_start: 0.7982 (tt0) cc_final: 0.7728 (tt0) REVERT: H 61 GLU cc_start: 0.7766 (mp0) cc_final: 0.7231 (mp0) REVERT: I 2 ASP cc_start: 0.8095 (m-30) cc_final: 0.7771 (m-30) REVERT: I 65 ASN cc_start: 0.8578 (m110) cc_final: 0.8349 (m-40) REVERT: J 65 ASN cc_start: 0.8526 (m110) cc_final: 0.7974 (m110) outliers start: 43 outliers final: 39 residues processed: 181 average time/residue: 1.2072 time to fit residues: 229.5498 Evaluate side-chains 204 residues out of total 690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 162 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 98 ASP Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.108391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.093135 restraints weight = 9280.618| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.32 r_work: 0.3265 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6950 Z= 0.264 Angle : 0.542 5.825 9320 Z= 0.299 Chirality : 0.050 0.123 1160 Planarity : 0.002 0.015 1170 Dihedral : 5.251 17.661 990 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 6.09 % Allowed : 21.88 % Favored : 72.03 % 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: -3.72 (0.22), residues: 970 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.17), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 50 PHE 0.017 0.004 PHE D 4 TYR 0.013 0.003 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3407.42 seconds wall clock time: 61 minutes 32.34 seconds (3692.34 seconds total)