Starting phenix.real_space_refine on Fri Sep 27 22:57:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/09_2024/8kef_37154_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/09_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_37154/09_2024/8kef_37154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/09_2024/8kef_37154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/09_2024/8kef_37154_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kef_37154/09_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. Time to flip 54 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17802 Number of models: 1 Model: "" Number of chains: 2 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: "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} Restraints were copied for chains: C, B, E, D, F, f, c, b, e, d Time building chain proxies: 6.18, per 1000 atoms: 0.35 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.2 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: 1.82 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: 4.19 Time building geometry restraints manager: 4.81 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: 0.00 - 1.93: 18088 1.93 - 3.87: 5430 3.87 - 5.80: 1082 5.80 - 7.74: 138 7.74 - 9.67: 36 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 33.290 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- 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 : 2.188 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: 0.2815 time to fit residues: 141.0089 Evaluate side-chains 259 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 2.280 ------------------------------------------------------------------------------- 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 : 2.466 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: 0.2880 time to fit residues: 107.3936 Evaluate side-chains 227 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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: 8.9990 chunk 167 optimal weight: 0.3980 chunk 137 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 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: 2.4186 ------------------------------------------------------------------------------- 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: 0.7233 moved from start: 0.1911 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= 0.190 Angle : 0.572 7.463 24774 Z= 0.290 Chirality : 0.048 0.176 2922 Planarity : 0.005 0.049 3174 Dihedral : 4.581 19.917 2392 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: -0.23 (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 D 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 309 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 234 time to evaluate : 2.045 Fit side-chains REVERT: C 18 GLU cc_start: 0.4129 (mp0) cc_final: 0.3746 (mp0) REVERT: F 18 GLU cc_start: 0.4137 (mp0) cc_final: 0.3756 (mp0) REVERT: a 117 TYR cc_start: 0.7627 (m-80) cc_final: 0.7324 (m-80) REVERT: b 118 GLN cc_start: 0.7510 (tp-100) cc_final: 0.6733 (pm20) REVERT: d 117 TYR cc_start: 0.7622 (m-80) cc_final: 0.7320 (m-80) REVERT: e 118 GLN cc_start: 0.7507 (tp-100) cc_final: 0.6738 (pm20) outliers start: 75 outliers final: 43 residues processed: 285 average time/residue: 0.2968 time to fit residues: 127.5818 Evaluate side-chains 257 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 214 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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: 4.9990 chunk 151 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18174 Z= 0.302 Angle : 0.606 7.558 24774 Z= 0.303 Chirality : 0.049 0.180 2922 Planarity : 0.005 0.047 3174 Dihedral : 4.676 25.639 2392 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.68 % Allowed : 21.12 % 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: -0.20 (0.18), residues: 2202 helix: 0.80 (0.31), residues: 258 sheet: -0.40 (0.21), residues: 516 loop : -0.13 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP a 184 HIS 0.004 0.002 HIS a 14 PHE 0.007 0.001 PHE a 78 TYR 0.013 0.001 TYR a 117 ARG 0.008 0.000 ARG C 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 273 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 217 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 118 GLN cc_start: 0.7637 (tp-100) cc_final: 0.7049 (pm20) REVERT: e 118 GLN cc_start: 0.7632 (tp-100) cc_final: 0.7053 (pm20) outliers start: 56 outliers final: 43 residues processed: 257 average time/residue: 0.2907 time to fit residues: 112.5609 Evaluate side-chains 250 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 2.117 ------------------------------------------------------------------------------- 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 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 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 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 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 b residue 193 ILE Chi-restraints excluded: chain c residue 36 VAL 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 e residue 193 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 193 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.5345 > 50: distance: 37 - 41: 11.499 distance: 41 - 42: 26.615 distance: 42 - 43: 12.186 distance: 42 - 45: 26.197 distance: 43 - 44: 16.614 distance: 43 - 49: 11.345 distance: 45 - 46: 21.992 distance: 46 - 47: 32.305 distance: 46 - 48: 14.253 distance: 49 - 50: 17.494 distance: 50 - 51: 25.177 distance: 50 - 53: 29.789 distance: 51 - 52: 27.438 distance: 51 - 57: 15.424 distance: 53 - 54: 21.666 distance: 54 - 56: 24.370 distance: 57 - 58: 18.345 distance: 57 - 63: 6.871 distance: 58 - 59: 36.121 distance: 58 - 61: 22.560 distance: 59 - 60: 15.504 distance: 59 - 64: 17.604 distance: 61 - 62: 22.613 distance: 62 - 63: 17.752 distance: 64 - 65: 27.825 distance: 65 - 66: 25.102 distance: 65 - 68: 10.178 distance: 66 - 67: 21.300 distance: 66 - 72: 18.013 distance: 68 - 69: 9.266 distance: 68 - 70: 22.804 distance: 69 - 71: 24.859 distance: 72 - 73: 7.160 distance: 73 - 74: 12.507 distance: 73 - 76: 20.366 distance: 74 - 75: 14.031 distance: 74 - 79: 10.447 distance: 76 - 77: 18.215 distance: 76 - 78: 24.563 distance: 79 - 80: 11.645 distance: 79 - 85: 8.012 distance: 80 - 81: 15.309 distance: 80 - 83: 21.137 distance: 81 - 82: 4.868 distance: 81 - 86: 22.655 distance: 83 - 84: 24.160 distance: 84 - 85: 4.473 distance: 86 - 87: 11.509 distance: 87 - 88: 22.186 distance: 87 - 90: 13.193 distance: 88 - 89: 18.904 distance: 88 - 95: 26.783 distance: 90 - 91: 30.009 distance: 91 - 92: 12.818 distance: 92 - 93: 13.433 distance: 92 - 94: 7.149 distance: 95 - 96: 7.873 distance: 96 - 97: 14.239 distance: 96 - 99: 14.490 distance: 97 - 98: 13.847 distance: 97 - 104: 16.119 distance: 99 - 100: 11.555 distance: 100 - 101: 26.980 distance: 101 - 102: 17.502 distance: 101 - 103: 33.639 distance: 104 - 105: 24.413 distance: 104 - 110: 27.665 distance: 105 - 106: 18.550 distance: 105 - 108: 37.688 distance: 106 - 107: 13.950 distance: 108 - 109: 36.183 distance: 109 - 110: 13.903 distance: 111 - 112: 15.620 distance: 112 - 113: 17.120 distance: 112 - 115: 14.748 distance: 113 - 114: 8.299 distance: 113 - 122: 29.985 distance: 115 - 116: 10.621 distance: 116 - 117: 17.319 distance: 116 - 118: 3.459 distance: 117 - 119: 15.154 distance: 118 - 120: 13.885 distance: 119 - 121: 9.047 distance: 120 - 121: 19.381