Starting phenix.real_space_refine on Mon Jul 22 07:20:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/07_2024/8kef_37154_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/07_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_37154/07_2024/8kef_37154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/07_2024/8kef_37154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/07_2024/8kef_37154_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/07_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 9.95, per 1000 atoms: 0.56 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: 6.43 Conformation dependent library (CDL) restraints added in 3.5 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: 1.93 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: 4.96 Time building geometry restraints manager: 7.00 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 2.520 nonbonded pdb=" N ILE a 193 " pdb=" OD1 ASN f 16 " model vdw 1.990 2.520 nonbonded pdb=" OD1 ASN c 16 " pdb=" N ILE d 193 " model vdw 1.990 2.520 nonbonded pdb=" OD1 ASN b 16 " pdb=" N ILE c 193 " model vdw 1.990 2.520 nonbonded pdb=" OD1 ASN e 16 " pdb=" N ILE f 193 " model vdw 1.990 2.520 ... (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 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: 1.040 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 47.980 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.110 ------------------------------------------------------------------------------- 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 : 2.181 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: 0.2923 time to fit residues: 146.8770 Evaluate side-chains 259 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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: 2.9990 chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** B 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18174 Z= 0.194 Angle : 0.588 7.139 24774 Z= 0.304 Chirality : 0.048 0.159 2922 Planarity : 0.006 0.060 3174 Dihedral : 4.813 19.875 2394 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.11 % Allowed : 19.16 % Favored : 78.74 % 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: -0.10 (0.18), residues: 2202 helix: 1.38 (0.32), residues: 258 sheet: 0.14 (0.22), residues: 516 loop : -0.39 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 84 HIS 0.003 0.001 HIS e 95 PHE 0.012 0.001 PHE a 78 TYR 0.016 0.001 TYR A 120 ARG 0.005 0.000 ARG F 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 272 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 228 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 34 residues processed: 264 average time/residue: 0.2929 time to fit residues: 117.3963 Evaluate side-chains 256 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 185 GLU Chi-restraints excluded: chain a residue 191 ASP 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 185 GLU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain b residue 193 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 185 GLU Chi-restraints excluded: chain d residue 191 ASP 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 e residue 185 GLU Chi-restraints excluded: chain e residue 191 ASP Chi-restraints excluded: chain e residue 193 ILE 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: 6.9990 chunk 62 optimal weight: 9.9990 chunk 167 optimal weight: 0.0770 chunk 137 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 218 optimal weight: 20.0000 chunk 179 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 overall best weight: 2.7942 ------------------------------------------------------------------------------- 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 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 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18174 Z= 0.188 Angle : 0.551 7.201 24774 Z= 0.277 Chirality : 0.048 0.175 2922 Planarity : 0.005 0.050 3174 Dihedral : 4.505 27.677 2392 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.54 % Allowed : 20.11 % Favored : 76.34 % 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: 0.12 (0.18), residues: 2202 helix: 1.38 (0.32), residues: 258 sheet: 0.49 (0.25), residues: 444 loop : -0.25 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 84 HIS 0.003 0.002 HIS a 14 PHE 0.009 0.001 PHE a 78 TYR 0.012 0.001 TYR B 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 296 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 222 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 118 GLN cc_start: 0.7511 (tp-100) cc_final: 0.6742 (pm20) REVERT: e 118 GLN cc_start: 0.7503 (tp-100) cc_final: 0.6744 (pm20) outliers start: 74 outliers final: 40 residues processed: 280 average time/residue: 0.2803 time to fit residues: 120.7990 Evaluate side-chains 244 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 82 GLU Chi-restraints excluded: chain B residue 123 ILE 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 82 GLU 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 191 ASP 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 b residue 191 ASP Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 191 ASP 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 e residue 191 ASP Chi-restraints excluded: chain f residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 22 optimal weight: 0.0970 chunk 96 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 overall best weight: 1.9582 ------------------------------------------------------------------------------- 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** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18174 Z= 0.169 Angle : 0.544 6.976 24774 Z= 0.272 Chirality : 0.048 0.175 2922 Planarity : 0.005 0.046 3174 Dihedral : 4.280 20.252 2390 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.11 % Allowed : 21.65 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2202 helix: 1.34 (0.32), residues: 258 sheet: 0.45 (0.24), residues: 444 loop : -0.28 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 90 HIS 0.002 0.001 HIS b 95 PHE 0.007 0.001 PHE d 78 TYR 0.012 0.001 TYR D 120 ARG 0.002 0.000 ARG C 78 *********************** 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 266 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 118 GLN cc_start: 0.7526 (tp-100) cc_final: 0.6739 (pm20) REVERT: e 118 GLN cc_start: 0.7521 (tp-100) cc_final: 0.6744 (pm20) outliers start: 44 outliers final: 32 residues processed: 254 average time/residue: 0.2971 time to fit residues: 115.1760 Evaluate side-chains 243 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 211 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 B residue 41 THR 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 82 GLU 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 75 ASP Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 41 THR 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 82 GLU 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 191 ASP Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain b residue 191 ASP Chi-restraints excluded: chain d residue 191 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 237 GLU Chi-restraints excluded: chain e residue 191 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 9.9990 chunk 121 optimal weight: 0.0070 chunk 3 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 148 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 4.4006 ------------------------------------------------------------------------------- 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** B 106 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18174 Z= 0.244 Angle : 0.556 7.036 24774 Z= 0.276 Chirality : 0.047 0.176 2922 Planarity : 0.004 0.044 3174 Dihedral : 4.310 23.905 2390 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.45 % Allowed : 20.07 % 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: 0.05 (0.18), residues: 2202 helix: 1.23 (0.32), residues: 258 sheet: 0.36 (0.24), residues: 444 loop : -0.26 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 90 HIS 0.003 0.001 HIS c 14 PHE 0.007 0.001 PHE c 171 TYR 0.010 0.001 TYR D 120 ARG 0.003 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 286 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 214 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 118 GLN cc_start: 0.7754 (tp-100) cc_final: 0.7163 (pm20) REVERT: e 118 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7163 (pm20) outliers start: 72 outliers final: 52 residues processed: 268 average time/residue: 0.2828 time to fit residues: 115.6616 Evaluate side-chains 254 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 202 time to evaluate : 2.163 ------------------------------------------------------------------------------- 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 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 75 ASP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 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 75 ASP 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 75 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 100 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 191 ASP 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 b residue 191 ASP Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 191 ASP 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 e residue 191 ASP Chi-restraints excluded: chain f residue 36 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.304 > 50: distance: 37 - 41: 30.157 distance: 41 - 42: 37.075 distance: 42 - 43: 44.636 distance: 42 - 45: 5.808 distance: 43 - 44: 36.857 distance: 43 - 49: 47.023 distance: 45 - 46: 17.342 distance: 46 - 47: 41.108 distance: 46 - 48: 26.001 distance: 49 - 50: 38.577 distance: 50 - 51: 34.705 distance: 50 - 53: 50.711 distance: 51 - 52: 24.986 distance: 51 - 57: 19.385 distance: 53 - 54: 7.760 distance: 54 - 55: 21.483 distance: 54 - 56: 35.842 distance: 57 - 63: 11.191 distance: 58 - 59: 60.705 distance: 58 - 61: 14.919 distance: 59 - 60: 14.073 distance: 59 - 64: 39.812 distance: 61 - 62: 16.091 distance: 62 - 63: 27.062 distance: 64 - 65: 46.611 distance: 65 - 66: 29.941 distance: 65 - 68: 28.438 distance: 66 - 67: 30.740 distance: 66 - 72: 11.963 distance: 68 - 69: 38.975 distance: 68 - 70: 43.279 distance: 69 - 71: 17.086 distance: 72 - 73: 22.402 distance: 73 - 74: 42.462 distance: 73 - 76: 50.953 distance: 74 - 75: 37.208 distance: 74 - 79: 54.035 distance: 76 - 77: 24.608 distance: 76 - 78: 54.984 distance: 79 - 80: 25.872 distance: 79 - 85: 21.296 distance: 80 - 81: 37.095 distance: 80 - 83: 37.951 distance: 81 - 86: 19.849 distance: 83 - 84: 54.054 distance: 84 - 85: 4.933 distance: 86 - 87: 16.114 distance: 87 - 88: 47.439 distance: 87 - 90: 8.534 distance: 88 - 89: 31.475 distance: 88 - 95: 18.673 distance: 90 - 91: 40.505 distance: 91 - 92: 5.479 distance: 92 - 93: 12.079 distance: 92 - 94: 8.435 distance: 95 - 96: 48.804 distance: 96 - 97: 20.452 distance: 97 - 98: 12.841 distance: 97 - 104: 19.951 distance: 99 - 100: 20.008 distance: 100 - 101: 44.278 distance: 101 - 102: 6.653 distance: 101 - 103: 58.775 distance: 104 - 105: 40.419 distance: 104 - 110: 55.398 distance: 105 - 106: 3.809 distance: 105 - 108: 54.402 distance: 106 - 107: 47.239 distance: 106 - 111: 41.067 distance: 108 - 109: 39.912 distance: 111 - 112: 5.635 distance: 112 - 113: 24.842 distance: 112 - 115: 6.912 distance: 113 - 114: 10.447 distance: 113 - 122: 29.591 distance: 115 - 116: 7.635 distance: 116 - 117: 34.703 distance: 117 - 119: 36.045 distance: 118 - 120: 16.313 distance: 119 - 121: 24.175 distance: 120 - 121: 30.267