Starting phenix.real_space_refine on Tue Aug 6 19:35:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/08_2024/8kef_37154_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/08_2024/8kef_37154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/08_2024/8kef_37154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/08_2024/8kef_37154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/08_2024/8kef_37154_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/08_2024/8kef_37154_neut.cif" } resolution = 3.44 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= 0.001 sd= 0.001 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 54 5.16 5 C 11442 2.51 5 N 2922 2.21 5 O 3384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ASP 121": "OD1" <-> "OD2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ASP 121": "OD1" <-> "OD2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 59": "OD1" <-> "OD2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F ASP 121": "OD1" <-> "OD2" Residue "a GLU 55": "OE1" <-> "OE2" Residue "a GLU 212": "OE1" <-> "OE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b GLU 212": "OE1" <-> "OE2" Residue "c GLU 55": "OE1" <-> "OE2" Residue "c GLU 212": "OE1" <-> "OE2" Residue "d GLU 55": "OE1" <-> "OE2" Residue "d GLU 212": "OE1" <-> "OE2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e GLU 212": "OE1" <-> "OE2" Residue "f GLU 55": "OE1" <-> "OE2" Residue "f GLU 212": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17802 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "C" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "D" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "E" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "F" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "a" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1926 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 220} Chain: "b" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1926 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 220} Chain: "c" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1926 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 220} Chain: "d" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1926 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 220} Chain: "e" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1926 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 220} Chain: "f" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1926 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 220} Time building chain proxies: 9.52, per 1000 atoms: 0.53 Number of scatterers: 17802 At special positions: 0 Unit cell: (148.73, 150.87, 128.4, 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 54 16.00 O 3384 8.00 N 2922 7.00 C 11442 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: 6.22 Conformation dependent library (CDL) restraints added in 3.1 seconds 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 24 sheets defined 20.8% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 4.125A pdb=" N ASN A 8 " --> pdb=" O SER A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 20 Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'B' and resid 4 through 15 removed outlier: 4.126A pdb=" N ASN B 8 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 20 Processing helix chain 'B' and resid 81 through 87 Processing helix chain 'C' and resid 4 through 15 removed outlier: 4.125A pdb=" N ASN C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'D' and resid 4 through 15 removed outlier: 4.125A pdb=" N ASN D 8 " --> pdb=" O SER D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 81 through 87 Processing helix chain 'E' and resid 4 through 15 removed outlier: 4.126A pdb=" N ASN E 8 " --> pdb=" O SER E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 81 through 87 Processing helix chain 'F' and resid 4 through 15 removed outlier: 4.126A pdb=" N ASN F 8 " --> pdb=" O SER F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 Processing helix chain 'F' and resid 81 through 87 Processing helix chain 'a' and resid 2 through 16 Processing helix chain 'a' and resid 93 through 97 Processing helix chain 'a' and resid 98 through 116 Processing helix chain 'a' and resid 116 through 121 removed outlier: 3.921A pdb=" N ASP a 121 " --> pdb=" O TYR a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 171 No H-bonds generated for 'chain 'a' and resid 169 through 171' Processing helix chain 'a' and resid 233 through 237 Processing helix chain 'b' and resid 2 through 16 Processing helix chain 'b' and resid 93 through 97 Processing helix chain 'b' and resid 98 through 116 Processing helix chain 'b' and resid 116 through 121 removed outlier: 3.921A pdb=" N ASP b 121 " --> pdb=" O TYR b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 171 No H-bonds generated for 'chain 'b' and resid 169 through 171' Processing helix chain 'b' and resid 233 through 237 Processing helix chain 'c' and resid 2 through 16 Processing helix chain 'c' and resid 93 through 97 Processing helix chain 'c' and resid 98 through 116 Processing helix chain 'c' and resid 116 through 121 removed outlier: 3.921A pdb=" N ASP c 121 " --> pdb=" O TYR c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 169 through 171 No H-bonds generated for 'chain 'c' and resid 169 through 171' Processing helix chain 'c' and resid 233 through 237 Processing helix chain 'd' and resid 2 through 16 Processing helix chain 'd' and resid 93 through 97 Processing helix chain 'd' and resid 98 through 116 Processing helix chain 'd' and resid 116 through 121 removed outlier: 3.921A pdb=" N ASP d 121 " --> pdb=" O TYR d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 169 through 171 No H-bonds generated for 'chain 'd' and resid 169 through 171' Processing helix chain 'd' and resid 233 through 237 Processing helix chain 'e' and resid 2 through 16 Processing helix chain 'e' and resid 93 through 97 Processing helix chain 'e' and resid 98 through 116 Processing helix chain 'e' and resid 116 through 121 removed outlier: 3.921A pdb=" N ASP e 121 " --> pdb=" O TYR e 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 169 through 171 No H-bonds generated for 'chain 'e' and resid 169 through 171' Processing helix chain 'e' and resid 233 through 237 Processing helix chain 'f' and resid 2 through 16 Processing helix chain 'f' and resid 93 through 97 Processing helix chain 'f' and resid 98 through 116 Processing helix chain 'f' and resid 116 through 121 removed outlier: 3.921A pdb=" N ASP f 121 " --> pdb=" O TYR f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 169 through 171 No H-bonds generated for 'chain 'f' and resid 169 through 171' Processing helix chain 'f' and resid 233 through 237 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 removed outlier: 5.368A pdb=" N CYS A 109 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG A 125 " --> pdb=" O CYS A 109 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU A 122 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR A 74 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A 124 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR A 72 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS A 126 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A 70 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 66 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET A 53 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 68 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS A 51 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 70 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 49 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39 removed outlier: 5.369A pdb=" N CYS B 109 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG B 125 " --> pdb=" O CYS B 109 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU B 122 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR B 74 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU B 124 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR B 72 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS B 126 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP B 70 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 66 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET B 53 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 68 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS B 51 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP B 70 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 49 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 39 removed outlier: 5.369A pdb=" N CYS C 109 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG C 125 " --> pdb=" O CYS C 109 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU C 122 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR C 74 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU C 124 " --> pdb=" O TYR C 72 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR C 72 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS C 126 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP C 70 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 66 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET C 53 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA C 68 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS C 51 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP C 70 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL C 49 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 38 through 39 removed outlier: 5.368A pdb=" N CYS D 109 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG D 125 " --> pdb=" O CYS D 109 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU D 122 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR D 74 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU D 124 " --> pdb=" O TYR D 72 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR D 72 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS D 126 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP D 70 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE D 66 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET D 53 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA D 68 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS D 51 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP D 70 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 49 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 38 through 39 removed outlier: 5.369A pdb=" N CYS E 109 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG E 125 " --> pdb=" O CYS E 109 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU E 122 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR E 74 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU E 124 " --> pdb=" O TYR E 72 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TYR E 72 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS E 126 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP E 70 " --> pdb=" O LYS E 126 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE E 66 " --> pdb=" O MET E 53 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET E 53 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA E 68 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS E 51 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP E 70 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 49 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 38 through 39 removed outlier: 5.370A pdb=" N CYS F 109 " --> pdb=" O ARG F 125 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ARG F 125 " --> pdb=" O CYS F 109 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU F 122 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N THR F 74 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU F 124 " --> pdb=" O TYR F 72 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N TYR F 72 " --> pdb=" O LEU F 124 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS F 126 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP F 70 " --> pdb=" O LYS F 126 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE F 66 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET F 53 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA F 68 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS F 51 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP F 70 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 49 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 36 Processing sheet with id=AA8, first strand: chain 'a' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 44 through 48 current: chain 'a' and resid 71 through 86 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 71 through 86 current: chain 'a' and resid 150 through 167 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 205 through 211 removed outlier: 3.585A pdb=" N LEU a 208 " --> pdb=" O GLU a 228 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU a 228 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS a 210 " --> pdb=" O LEU a 226 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU a 226 " --> pdb=" O LYS a 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 34 through 36 Processing sheet with id=AB2, first strand: chain 'b' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 44 through 48 current: chain 'b' and resid 71 through 86 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 71 through 86 current: chain 'b' and resid 150 through 167 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'b' and resid 205 through 211 removed outlier: 3.586A pdb=" N LEU b 208 " --> pdb=" O GLU b 228 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU b 228 " --> pdb=" O LEU b 208 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS b 210 " --> pdb=" O LEU b 226 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU b 226 " --> pdb=" O LYS b 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 34 through 36 Processing sheet with id=AB5, first strand: chain 'c' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 44 through 48 current: chain 'c' and resid 71 through 86 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 71 through 86 current: chain 'c' and resid 150 through 167 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'c' and resid 205 through 211 removed outlier: 3.586A pdb=" N LEU c 208 " --> pdb=" O GLU c 228 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU c 228 " --> pdb=" O LEU c 208 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS c 210 " --> pdb=" O LEU c 226 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU c 226 " --> pdb=" O LYS c 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 34 through 36 Processing sheet with id=AB8, first strand: chain 'd' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 44 through 48 current: chain 'd' and resid 71 through 86 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 71 through 86 current: chain 'd' and resid 150 through 167 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'd' and resid 205 through 211 removed outlier: 3.585A pdb=" N LEU d 208 " --> pdb=" O GLU d 228 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU d 228 " --> pdb=" O LEU d 208 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS d 210 " --> pdb=" O LEU d 226 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU d 226 " --> pdb=" O LYS d 210 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 34 through 36 Processing sheet with id=AC2, first strand: chain 'e' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 44 through 48 current: chain 'e' and resid 71 through 86 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 71 through 86 current: chain 'e' and resid 150 through 167 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'e' and resid 205 through 211 removed outlier: 3.586A pdb=" N LEU e 208 " --> pdb=" O GLU e 228 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU e 228 " --> pdb=" O LEU e 208 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS e 210 " --> pdb=" O LEU e 226 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU e 226 " --> pdb=" O LYS e 210 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'f' and resid 34 through 36 Processing sheet with id=AC5, first strand: chain 'f' and resid 44 through 48 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 44 through 48 current: chain 'f' and resid 71 through 86 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 71 through 86 current: chain 'f' and resid 150 through 167 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'f' and resid 205 through 211 removed outlier: 3.586A pdb=" N LEU f 208 " --> pdb=" O GLU f 228 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU f 228 " --> pdb=" O LEU f 208 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS f 210 " --> pdb=" O LEU f 226 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU f 226 " --> pdb=" O LYS f 210 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 918 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: 4.16 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3018 1.30 - 1.43: 4391 1.43 - 1.57: 10625 1.57 - 1.70: 56 1.70 - 1.83: 84 Bond restraints: 18174 Sorted by residual: bond pdb=" C ARG E 17 " pdb=" O ARG E 17 " ideal model delta sigma weight residual 1.237 1.172 0.065 1.17e-02 7.31e+03 3.06e+01 bond pdb=" C ARG A 17 " pdb=" O ARG A 17 " ideal model delta sigma weight residual 1.237 1.172 0.064 1.17e-02 7.31e+03 3.02e+01 bond pdb=" C ARG D 17 " pdb=" O ARG D 17 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.17e-02 7.31e+03 3.01e+01 bond pdb=" C ARG F 17 " pdb=" O ARG F 17 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.17e-02 7.31e+03 3.01e+01 bond pdb=" C ARG C 17 " pdb=" O ARG C 17 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.17e-02 7.31e+03 3.01e+01 ... (remaining 18169 not shown) Histogram of bond angle deviations from ideal: 92.55 - 100.65: 25 100.65 - 108.75: 2267 108.75 - 116.85: 10691 116.85 - 124.95: 11234 124.95 - 133.05: 557 Bond angle restraints: 24774 Sorted by residual: angle pdb=" CA ASP A 22 " pdb=" CB ASP A 22 " pdb=" CG ASP A 22 " ideal model delta sigma weight residual 112.60 120.47 -7.87 1.00e+00 1.00e+00 6.20e+01 angle pdb=" CA ASP D 22 " pdb=" CB ASP D 22 " pdb=" CG ASP D 22 " ideal model delta sigma weight residual 112.60 120.47 -7.87 1.00e+00 1.00e+00 6.20e+01 angle pdb=" CA ASP F 22 " pdb=" CB ASP F 22 " pdb=" CG ASP F 22 " ideal model delta sigma weight residual 112.60 120.42 -7.82 1.00e+00 1.00e+00 6.12e+01 angle pdb=" CA ASP C 22 " pdb=" CB ASP C 22 " pdb=" CG ASP C 22 " ideal model delta sigma weight residual 112.60 120.42 -7.82 1.00e+00 1.00e+00 6.12e+01 angle pdb=" CA ASP B 22 " pdb=" CB ASP B 22 " pdb=" CG ASP B 22 " ideal model delta sigma weight residual 112.60 120.41 -7.81 1.00e+00 1.00e+00 6.11e+01 ... (remaining 24769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 9972 16.89 - 33.77: 944 33.77 - 50.66: 208 50.66 - 67.54: 54 67.54 - 84.43: 30 Dihedral angle restraints: 11208 sinusoidal: 4602 harmonic: 6606 Sorted by residual: dihedral pdb=" N TYR C 3 " pdb=" C TYR C 3 " pdb=" CA TYR C 3 " pdb=" CB TYR C 3 " ideal model delta harmonic sigma weight residual 122.80 136.15 -13.35 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" N TYR F 3 " pdb=" C TYR F 3 " pdb=" CA TYR F 3 " pdb=" CB TYR F 3 " ideal model delta harmonic sigma weight residual 122.80 136.15 -13.35 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" N TYR A 3 " pdb=" C TYR A 3 " pdb=" CA TYR A 3 " pdb=" CB TYR A 3 " ideal model delta harmonic sigma weight residual 122.80 136.13 -13.33 0 2.50e+00 1.60e-01 2.84e+01 ... (remaining 11205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2068 0.107 - 0.213: 687 0.213 - 0.319: 137 0.319 - 0.426: 12 0.426 - 0.532: 18 Chirality restraints: 2922 Sorted by residual: chirality pdb=" CA THR c 183 " pdb=" N THR c 183 " pdb=" C THR c 183 " pdb=" CB THR c 183 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CA THR f 183 " pdb=" N THR f 183 " pdb=" C THR f 183 " pdb=" CB THR f 183 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CA THR d 183 " pdb=" N THR d 183 " pdb=" C THR d 183 " pdb=" CB THR d 183 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 7.05e+00 ... (remaining 2919 not shown) Planarity restraints: 3174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 184 " 0.088 2.00e-02 2.50e+03 4.31e-02 4.65e+01 pdb=" CG TRP a 184 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP a 184 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP a 184 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP a 184 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP a 184 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP a 184 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 184 " 0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 184 " -0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP a 184 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP e 184 " -0.088 2.00e-02 2.50e+03 4.31e-02 4.65e+01 pdb=" CG TRP e 184 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP e 184 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP e 184 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP e 184 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP e 184 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP e 184 " 0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP e 184 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP e 184 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP e 184 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP d 184 " -0.088 2.00e-02 2.50e+03 4.31e-02 4.64e+01 pdb=" CG TRP d 184 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP d 184 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP d 184 " 0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP d 184 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP d 184 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP d 184 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 184 " -0.051 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 184 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP d 184 " -0.039 2.00e-02 2.50e+03 ... (remaining 3171 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 96 2.57 - 3.15: 13569 3.15 - 3.74: 27435 3.74 - 4.32: 38080 4.32 - 4.90: 61603 Nonbonded interactions: 140783 Sorted by model distance: nonbonded pdb=" OD1 ASN d 16 " pdb=" N ILE e 193 " model vdw 1.989 3.120 nonbonded pdb=" N ILE a 193 " pdb=" OD1 ASN f 16 " model vdw 1.990 3.120 nonbonded pdb=" OD1 ASN c 16 " pdb=" N ILE d 193 " model vdw 1.990 3.120 nonbonded pdb=" OD1 ASN b 16 " pdb=" N ILE c 193 " model vdw 1.990 3.120 nonbonded pdb=" OD1 ASN e 16 " pdb=" N ILE f 193 " model vdw 1.990 3.120 ... (remaining 140778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 44.050 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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 : 0.015 0.065 18174 Z= 1.012 Angle : 1.897 9.669 24774 Z= 1.299 Chirality : 0.113 0.532 2922 Planarity : 0.013 0.080 3174 Dihedral : 14.960 84.429 6888 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.44 % Allowed : 15.80 % Favored : 82.76 % Cbeta Deviations : 1.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2202 helix: 1.60 (0.26), residues: 264 sheet: 0.04 (0.21), residues: 564 loop : -0.91 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.022 TRP a 184 HIS 0.004 0.002 HIS B 110 PHE 0.038 0.011 PHE a 78 TYR 0.080 0.023 TYR e 94 ARG 0.030 0.007 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 309 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 118 GLN cc_start: 0.7231 (tp-100) cc_final: 0.6826 (pm20) REVERT: c 118 GLN cc_start: 0.7361 (tp-100) cc_final: 0.6866 (pm20) REVERT: e 118 GLN cc_start: 0.7223 (tp-100) cc_final: 0.6828 (pm20) REVERT: f 118 GLN cc_start: 0.7353 (tp-100) cc_final: 0.6868 (pm20) outliers start: 30 outliers final: 6 residues processed: 329 average time/residue: 0.2978 time to fit residues: 149.1314 Evaluate side-chains 259 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain f residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.9980 chunk 168 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 180 GLN ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 180 GLN ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 180 GLN ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 180 GLN ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 180 GLN ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18174 Z= 0.280 Angle : 0.616 6.765 24774 Z= 0.319 Chirality : 0.048 0.170 2922 Planarity : 0.006 0.058 3174 Dihedral : 4.925 20.058 2394 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.53 % Allowed : 19.92 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2202 helix: 1.03 (0.31), residues: 258 sheet: -0.07 (0.22), residues: 516 loop : -0.31 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 84 HIS 0.004 0.001 HIS a 14 PHE 0.010 0.001 PHE e 78 TYR 0.013 0.001 TYR A 120 ARG 0.005 0.001 ARG C 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 117 TYR cc_start: 0.7786 (m-80) cc_final: 0.7534 (m-80) REVERT: d 117 TYR cc_start: 0.7779 (m-80) cc_final: 0.7536 (m-80) outliers start: 32 outliers final: 23 residues processed: 244 average time/residue: 0.2927 time to fit residues: 108.8667 Evaluate side-chains 227 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 193 ILE Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 237 GLU Chi-restraints excluded: chain f residue 193 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 0.1980 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 218 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 200 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18174 Z= 0.186 Angle : 0.571 7.447 24774 Z= 0.290 Chirality : 0.048 0.179 2922 Planarity : 0.005 0.049 3174 Dihedral : 4.581 19.895 2392 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.59 % Allowed : 18.92 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2202 helix: 1.09 (0.31), residues: 258 sheet: -0.22 (0.22), residues: 516 loop : -0.14 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 84 HIS 0.003 0.001 HIS b 95 PHE 0.011 0.001 PHE c 78 TYR 0.012 0.001 TYR A 120 ARG 0.002 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 235 time to evaluate : 2.329 Fit side-chains REVERT: C 18 GLU cc_start: 0.4128 (mp0) cc_final: 0.3722 (mp0) REVERT: F 18 GLU cc_start: 0.4138 (mp0) cc_final: 0.3731 (mp0) REVERT: a 117 TYR cc_start: 0.7625 (m-80) cc_final: 0.7322 (m-80) REVERT: b 118 GLN cc_start: 0.7509 (tp-100) cc_final: 0.6734 (pm20) REVERT: d 117 TYR cc_start: 0.7621 (m-80) cc_final: 0.7317 (m-80) REVERT: e 118 GLN cc_start: 0.7506 (tp-100) cc_final: 0.6740 (pm20) outliers start: 75 outliers final: 43 residues processed: 286 average time/residue: 0.2975 time to fit residues: 128.3087 Evaluate side-chains 260 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 113 ASN Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 237 GLU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 193 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 40.0000 chunk 96 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 192 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN B 79 ASN ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18174 Z= 0.200 Angle : 0.573 7.330 24774 Z= 0.289 Chirality : 0.049 0.178 2922 Planarity : 0.005 0.046 3174 Dihedral : 4.521 26.406 2392 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.83 % Allowed : 20.69 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.18), residues: 2202 helix: 0.96 (0.31), residues: 258 sheet: 0.17 (0.24), residues: 444 loop : -0.17 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 184 HIS 0.003 0.001 HIS b 95 PHE 0.008 0.001 PHE a 78 TYR 0.011 0.001 TYR D 120 ARG 0.008 0.000 ARG F 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 227 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 118 GLN cc_start: 0.7563 (tp-100) cc_final: 0.6876 (pm20) REVERT: e 118 GLN cc_start: 0.7556 (tp-100) cc_final: 0.6880 (pm20) outliers start: 59 outliers final: 41 residues processed: 268 average time/residue: 0.3138 time to fit residues: 126.8878 Evaluate side-chains 260 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 237 GLU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 193 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 148 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 192 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 ASN E 79 ASN ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18174 Z= 0.167 Angle : 0.559 7.322 24774 Z= 0.281 Chirality : 0.048 0.183 2922 Planarity : 0.004 0.045 3174 Dihedral : 4.350 24.513 2392 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.97 % Allowed : 20.83 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 2202 helix: 0.98 (0.31), residues: 258 sheet: 0.19 (0.24), residues: 444 loop : -0.20 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 90 HIS 0.002 0.001 HIS a 95 PHE 0.008 0.001 PHE a 78 TYR 0.011 0.001 TYR D 120 ARG 0.002 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 244 time to evaluate : 2.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.4204 (mp0) cc_final: 0.3872 (mp0) REVERT: B 18 GLU cc_start: 0.4051 (mp0) cc_final: 0.3642 (mp0) REVERT: C 18 GLU cc_start: 0.4175 (mp0) cc_final: 0.3759 (mp0) REVERT: D 18 GLU cc_start: 0.4161 (mp0) cc_final: 0.3829 (mp0) REVERT: E 18 GLU cc_start: 0.4157 (mp0) cc_final: 0.3732 (mp0) REVERT: F 18 GLU cc_start: 0.4190 (mp0) cc_final: 0.3774 (mp0) REVERT: a 118 GLN cc_start: 0.5173 (pm20) cc_final: 0.4937 (pm20) REVERT: b 118 GLN cc_start: 0.7572 (tp-100) cc_final: 0.6879 (pm20) REVERT: d 118 GLN cc_start: 0.5174 (pm20) cc_final: 0.4930 (pm20) REVERT: e 118 GLN cc_start: 0.7567 (tp-100) cc_final: 0.6881 (pm20) outliers start: 62 outliers final: 40 residues processed: 293 average time/residue: 0.2877 time to fit residues: 127.4894 Evaluate side-chains 260 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 237 GLU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 193 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN E 113 ASN ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18174 Z= 0.290 Angle : 0.598 7.757 24774 Z= 0.298 Chirality : 0.049 0.188 2922 Planarity : 0.004 0.043 3174 Dihedral : 4.562 41.115 2390 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.07 % Allowed : 21.26 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 2202 helix: 0.85 (0.31), residues: 258 sheet: -0.02 (0.23), residues: 438 loop : -0.15 (0.18), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 90 HIS 0.006 0.002 HIS d 14 PHE 0.010 0.001 PHE E 85 TYR 0.012 0.001 TYR d 117 ARG 0.003 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 216 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 118 GLN cc_start: 0.7693 (tp-100) cc_final: 0.7263 (pm20) REVERT: e 118 GLN cc_start: 0.7692 (tp-100) cc_final: 0.7264 (pm20) outliers start: 64 outliers final: 42 residues processed: 268 average time/residue: 0.3058 time to fit residues: 122.7968 Evaluate side-chains 257 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 215 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 122 optimal weight: 0.0050 chunk 156 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 overall best weight: 0.9936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 16 ASN ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 16 ASN ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18174 Z= 0.168 Angle : 0.566 7.180 24774 Z= 0.284 Chirality : 0.048 0.177 2922 Planarity : 0.004 0.040 3174 Dihedral : 4.372 41.465 2390 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.97 % Allowed : 21.12 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 2202 helix: 1.12 (0.31), residues: 258 sheet: 0.02 (0.24), residues: 444 loop : -0.23 (0.18), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 90 HIS 0.002 0.001 HIS a 14 PHE 0.007 0.001 PHE c 78 TYR 0.023 0.001 TYR B 120 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 247 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.4088 (mp0) cc_final: 0.3725 (mp0) REVERT: B 18 GLU cc_start: 0.4178 (mp0) cc_final: 0.3730 (mp0) REVERT: C 18 GLU cc_start: 0.4063 (mp0) cc_final: 0.3627 (mp0) REVERT: D 18 GLU cc_start: 0.4111 (mp0) cc_final: 0.3737 (mp0) REVERT: E 18 GLU cc_start: 0.4172 (mp0) cc_final: 0.3721 (mp0) REVERT: F 18 GLU cc_start: 0.4059 (mp0) cc_final: 0.3636 (mp0) REVERT: b 118 GLN cc_start: 0.7626 (tp-100) cc_final: 0.7189 (pm20) REVERT: c 118 GLN cc_start: 0.7462 (tp-100) cc_final: 0.7069 (pm20) REVERT: e 118 GLN cc_start: 0.7621 (tp-100) cc_final: 0.7194 (pm20) REVERT: f 118 GLN cc_start: 0.7474 (tp-100) cc_final: 0.7008 (pm20) outliers start: 62 outliers final: 39 residues processed: 297 average time/residue: 0.3004 time to fit residues: 134.5228 Evaluate side-chains 270 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 237 GLU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18174 Z= 0.338 Angle : 0.620 7.850 24774 Z= 0.309 Chirality : 0.049 0.190 2922 Planarity : 0.004 0.041 3174 Dihedral : 4.501 33.117 2390 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.73 % Allowed : 21.31 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 2202 helix: 0.97 (0.31), residues: 258 sheet: -0.52 (0.21), residues: 516 loop : -0.16 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 90 HIS 0.006 0.002 HIS d 14 PHE 0.009 0.001 PHE c 78 TYR 0.026 0.002 TYR E 120 ARG 0.005 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 217 time to evaluate : 2.567 Fit side-chains REVERT: A 18 GLU cc_start: 0.4103 (mp0) cc_final: 0.3673 (mp0) REVERT: B 18 GLU cc_start: 0.4319 (mp0) cc_final: 0.3820 (mp0) REVERT: D 18 GLU cc_start: 0.4132 (mp0) cc_final: 0.3689 (mp0) REVERT: E 18 GLU cc_start: 0.4308 (mp0) cc_final: 0.3811 (mp0) REVERT: b 118 GLN cc_start: 0.7719 (tp-100) cc_final: 0.7240 (pm20) REVERT: e 118 GLN cc_start: 0.7718 (tp-100) cc_final: 0.7246 (pm20) outliers start: 57 outliers final: 41 residues processed: 262 average time/residue: 0.3177 time to fit residues: 122.5131 Evaluate side-chains 252 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 156 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18174 Z= 0.299 Angle : 0.610 8.548 24774 Z= 0.305 Chirality : 0.049 0.217 2922 Planarity : 0.004 0.040 3174 Dihedral : 4.610 37.538 2390 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.06 % Allowed : 22.22 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2202 helix: 0.86 (0.31), residues: 258 sheet: -0.64 (0.21), residues: 516 loop : -0.21 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 90 HIS 0.005 0.001 HIS d 14 PHE 0.009 0.001 PHE c 78 TYR 0.024 0.002 TYR F 120 ARG 0.004 0.000 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 212 time to evaluate : 2.237 Fit side-chains REVERT: A 18 GLU cc_start: 0.4198 (mp0) cc_final: 0.3787 (mp0) REVERT: C 18 GLU cc_start: 0.4117 (mp0) cc_final: 0.3883 (mp0) REVERT: D 18 GLU cc_start: 0.4191 (mp0) cc_final: 0.3784 (mp0) REVERT: F 18 GLU cc_start: 0.4091 (mp0) cc_final: 0.3873 (mp0) REVERT: b 118 GLN cc_start: 0.7754 (tp-100) cc_final: 0.7306 (pm20) REVERT: c 118 GLN cc_start: 0.7732 (tp-100) cc_final: 0.7132 (pm20) REVERT: e 118 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7308 (pm20) REVERT: f 118 GLN cc_start: 0.7745 (tp-100) cc_final: 0.7149 (pm20) outliers start: 43 outliers final: 37 residues processed: 248 average time/residue: 0.3291 time to fit residues: 120.5802 Evaluate side-chains 252 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 193 ILE Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 193 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 146 optimal weight: 0.0000 chunk 221 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18174 Z= 0.198 Angle : 0.586 7.897 24774 Z= 0.293 Chirality : 0.049 0.206 2922 Planarity : 0.004 0.040 3174 Dihedral : 4.436 35.386 2390 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.82 % Allowed : 22.27 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 2202 helix: 1.04 (0.32), residues: 258 sheet: -0.54 (0.21), residues: 516 loop : -0.21 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 90 HIS 0.002 0.001 HIS a 95 PHE 0.006 0.001 PHE E 85 TYR 0.025 0.001 TYR B 120 ARG 0.004 0.000 ARG C 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 236 time to evaluate : 2.129 Fit side-chains REVERT: C 18 GLU cc_start: 0.4023 (mp0) cc_final: 0.3758 (mp0) REVERT: D 18 GLU cc_start: 0.4143 (mp0) cc_final: 0.3748 (mp0) REVERT: F 18 GLU cc_start: 0.4010 (mp0) cc_final: 0.3760 (mp0) REVERT: b 118 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7305 (pm20) REVERT: c 118 GLN cc_start: 0.7533 (tp-100) cc_final: 0.7074 (pm20) REVERT: e 118 GLN cc_start: 0.7677 (tp-100) cc_final: 0.7310 (pm20) REVERT: f 118 GLN cc_start: 0.7537 (tp-100) cc_final: 0.7095 (pm20) outliers start: 38 outliers final: 32 residues processed: 265 average time/residue: 0.3272 time to fit residues: 129.1940 Evaluate side-chains 261 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 162 optimal weight: 0.0970 chunk 26 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.063220 restraints weight = 62974.683| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.37 r_work: 0.3010 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18174 Z= 0.277 Angle : 0.606 7.909 24774 Z= 0.302 Chirality : 0.049 0.208 2922 Planarity : 0.005 0.071 3174 Dihedral : 4.471 34.738 2390 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.87 % Allowed : 22.13 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 2202 helix: 0.95 (0.31), residues: 258 sheet: -0.63 (0.21), residues: 516 loop : -0.21 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 184 HIS 0.004 0.001 HIS d 14 PHE 0.008 0.001 PHE E 85 TYR 0.023 0.001 TYR B 120 ARG 0.004 0.000 ARG E 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3550.47 seconds wall clock time: 64 minutes 24.92 seconds (3864.92 seconds total)