Starting phenix.real_space_refine on Sun Aug 24 05:45:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kef_37154/08_2025/8kef_37154_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kef_37154/08_2025/8kef_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/cci-nas-00/data/ceres_data/8kef_37154/08_2025/8kef_37154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kef_37154/08_2025/8kef_37154.map" model { file = "/net/cci-nas-00/data/ceres_data/8kef_37154/08_2025/8kef_37154_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kef_37154/08_2025/8kef_37154_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F, b, c, d, e, f Time building chain proxies: 2.21, per 1000 atoms: 0.12 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: 1.47 Conformation dependent library (CDL) restraints added in 737.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.57 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: 2.64 Time building geometry restraints manager: 1.93 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: 0.03 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: 1.230 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.760 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.310 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- 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= 0.896 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.030 0.007 ARG D 125 TYR 0.080 0.023 TYR e 94 PHE 0.038 0.011 PHE a 78 TRP 0.088 0.022 TRP a 184 HIS 0.004 0.002 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.01536 (18174) covalent geometry : angle 1.89670 (24774) hydrogen bonds : bond 0.17809 ( 396) hydrogen bonds : angle 6.99567 ( 918) *********************** 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 to be fit. rotamer outliers: 30 poor density : 309 time to evaluate : 0.747 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: 0.1289 time to fit residues: 64.9134 Evaluate side-chains 259 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 216 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.064321 restraints weight = 62505.580| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.46 r_work: 0.3032 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18174 Z= 0.174 Angle : 0.616 6.875 24774 Z= 0.319 Chirality : 0.049 0.168 2922 Planarity : 0.006 0.059 3174 Dihedral : 4.928 20.155 2394 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.53 % Allowed : 19.88 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.18), residues: 2202 helix: 1.05 (0.31), residues: 258 sheet: -0.05 (0.22), residues: 516 loop : -0.30 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 128 TYR 0.013 0.001 TYR A 120 PHE 0.011 0.001 PHE e 78 TRP 0.011 0.001 TRP a 84 HIS 0.003 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00409 (18174) covalent geometry : angle 0.61603 (24774) hydrogen bonds : bond 0.04743 ( 396) hydrogen bonds : angle 6.26205 ( 918) *********************** 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 252 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 MET cc_start: 0.8300 (tpt) cc_final: 0.7850 (tpt) REVERT: C 53 MET cc_start: 0.8371 (tpt) cc_final: 0.7818 (tpt) REVERT: E 53 MET cc_start: 0.8330 (tpt) cc_final: 0.7879 (tpt) REVERT: F 53 MET cc_start: 0.8362 (tpt) cc_final: 0.7809 (tpt) REVERT: f 16 ASN cc_start: 0.7599 (t0) cc_final: 0.7340 (t0) outliers start: 32 outliers final: 23 residues processed: 246 average time/residue: 0.1242 time to fit residues: 47.2612 Evaluate side-chains 230 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 4 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- 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 8 ASN B 79 ASN ** 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.064690 restraints weight = 62933.861| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.41 r_work: 0.3045 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18174 Z= 0.124 Angle : 0.573 7.420 24774 Z= 0.290 Chirality : 0.048 0.179 2922 Planarity : 0.005 0.049 3174 Dihedral : 4.585 20.074 2392 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.40 % Allowed : 18.97 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.18), residues: 2202 helix: 1.11 (0.31), residues: 258 sheet: 0.27 (0.24), residues: 444 loop : -0.21 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 128 TYR 0.012 0.001 TYR B 120 PHE 0.011 0.001 PHE c 78 TRP 0.006 0.001 TRP d 84 HIS 0.003 0.001 HIS b 95 Details of bonding type rmsd covalent geometry : bond 0.00292 (18174) covalent geometry : angle 0.57299 (24774) hydrogen bonds : bond 0.04039 ( 396) hydrogen bonds : angle 5.77490 ( 918) *********************** 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 306 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 235 time to evaluate : 0.629 Fit side-chains REVERT: A 53 MET cc_start: 0.8020 (tpt) cc_final: 0.7707 (tpt) REVERT: A 92 ASP cc_start: 0.8588 (m-30) cc_final: 0.8353 (m-30) REVERT: B 53 MET cc_start: 0.8285 (tpt) cc_final: 0.7803 (tpt) REVERT: C 18 GLU cc_start: 0.7817 (mp0) cc_final: 0.7250 (mp0) REVERT: C 53 MET cc_start: 0.8280 (tpt) cc_final: 0.7728 (tpt) REVERT: D 53 MET cc_start: 0.8039 (tpt) cc_final: 0.7730 (tpt) REVERT: D 92 ASP cc_start: 0.8586 (m-30) cc_final: 0.8352 (m-30) REVERT: E 53 MET cc_start: 0.8314 (tpt) cc_final: 0.7831 (tpt) REVERT: F 18 GLU cc_start: 0.7812 (mp0) cc_final: 0.7249 (mp0) REVERT: F 53 MET cc_start: 0.8283 (tpt) cc_final: 0.7731 (tpt) REVERT: b 118 GLN cc_start: 0.9061 (tp-100) cc_final: 0.7159 (pm20) REVERT: c 62 MET cc_start: 0.8274 (mtp) cc_final: 0.6743 (tpt) REVERT: e 118 GLN cc_start: 0.9058 (tp-100) cc_final: 0.7156 (pm20) REVERT: f 62 MET cc_start: 0.8265 (mtp) cc_final: 0.6727 (tpt) outliers start: 71 outliers final: 43 residues processed: 288 average time/residue: 0.1331 time to fit residues: 58.1730 Evaluate side-chains 260 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 9 optimal weight: 0.0870 chunk 4 optimal weight: 30.0000 chunk 221 optimal weight: 0.4980 chunk 208 optimal weight: 10.0000 chunk 35 optimal weight: 0.0040 chunk 127 optimal weight: 0.0370 overall best weight: 0.5250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 ASN E 79 ASN ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.075063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066385 restraints weight = 62538.543| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.41 r_work: 0.3085 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18174 Z= 0.107 Angle : 0.566 7.396 24774 Z= 0.285 Chirality : 0.049 0.183 2922 Planarity : 0.005 0.045 3174 Dihedral : 4.396 26.250 2392 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.63 % Allowed : 20.79 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 2202 helix: 1.00 (0.31), residues: 258 sheet: 0.28 (0.25), residues: 444 loop : -0.16 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 128 TYR 0.013 0.001 TYR D 120 PHE 0.009 0.001 PHE a 78 TRP 0.006 0.001 TRP A 90 HIS 0.003 0.001 HIS a 95 Details of bonding type rmsd covalent geometry : bond 0.00242 (18174) covalent geometry : angle 0.56617 (24774) hydrogen bonds : bond 0.03579 ( 396) hydrogen bonds : angle 5.68887 ( 918) *********************** 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 297 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7807 (mp0) cc_final: 0.7234 (mp0) REVERT: A 53 MET cc_start: 0.8043 (tpt) cc_final: 0.7582 (tpt) REVERT: A 92 ASP cc_start: 0.8559 (m-30) cc_final: 0.8309 (m-30) REVERT: B 18 GLU cc_start: 0.7630 (mp0) cc_final: 0.6991 (mp0) REVERT: B 53 MET cc_start: 0.8221 (tpt) cc_final: 0.7703 (tpt) REVERT: C 53 MET cc_start: 0.8170 (tpt) cc_final: 0.7593 (tpt) REVERT: D 18 GLU cc_start: 0.7772 (mp0) cc_final: 0.7194 (mp0) REVERT: D 53 MET cc_start: 0.8063 (tpt) cc_final: 0.7607 (tpt) REVERT: D 92 ASP cc_start: 0.8590 (m-30) cc_final: 0.8339 (m-30) REVERT: E 18 GLU cc_start: 0.7644 (mp0) cc_final: 0.7010 (mp0) REVERT: E 53 MET cc_start: 0.8255 (tpt) cc_final: 0.7737 (tpt) REVERT: F 53 MET cc_start: 0.8171 (tpt) cc_final: 0.7596 (tpt) REVERT: a 1 MET cc_start: 0.6316 (mpp) cc_final: 0.5925 (mtp) REVERT: a 169 ASP cc_start: 0.8663 (m-30) cc_final: 0.8455 (m-30) REVERT: b 62 MET cc_start: 0.7962 (ttm) cc_final: 0.6488 (tpt) REVERT: b 118 GLN cc_start: 0.8903 (tp-100) cc_final: 0.6933 (pm20) REVERT: c 62 MET cc_start: 0.8286 (mtp) cc_final: 0.6766 (tpt) REVERT: d 1 MET cc_start: 0.6328 (mpp) cc_final: 0.5937 (mtp) REVERT: d 169 ASP cc_start: 0.8661 (m-30) cc_final: 0.8455 (m-30) REVERT: e 62 MET cc_start: 0.7959 (ttm) cc_final: 0.6484 (tpt) REVERT: e 118 GLN cc_start: 0.8895 (tp-100) cc_final: 0.6924 (pm20) REVERT: f 62 MET cc_start: 0.8290 (mtp) cc_final: 0.6760 (tpt) outliers start: 55 outliers final: 37 residues processed: 285 average time/residue: 0.1354 time to fit residues: 58.9422 Evaluate side-chains 260 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 223 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 123 ILE Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain c residue 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 82 ILE Chi-restraints excluded: chain f residue 193 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 9 optimal weight: 0.0870 chunk 49 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 ASN E 113 ASN a 16 ASN ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 16 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065733 restraints weight = 62108.048| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.35 r_work: 0.3070 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2290 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= 0.116 Angle : 0.550 7.401 24774 Z= 0.275 Chirality : 0.048 0.180 2922 Planarity : 0.004 0.043 3174 Dihedral : 4.206 20.338 2390 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.73 % Allowed : 21.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 2202 helix: 1.06 (0.31), residues: 258 sheet: 0.24 (0.24), residues: 444 loop : -0.16 (0.17), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 78 TYR 0.011 0.001 TYR D 120 PHE 0.007 0.001 PHE d 78 TRP 0.005 0.001 TRP e 184 HIS 0.003 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00275 (18174) covalent geometry : angle 0.55021 (24774) hydrogen bonds : bond 0.03503 ( 396) hydrogen bonds : angle 5.46999 ( 918) *********************** 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 291 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 234 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8026 (tpt) cc_final: 0.7658 (tpt) REVERT: A 92 ASP cc_start: 0.8546 (m-30) cc_final: 0.8283 (m-30) REVERT: B 53 MET cc_start: 0.8205 (tpt) cc_final: 0.7705 (tpt) REVERT: C 18 GLU cc_start: 0.7776 (mp0) cc_final: 0.7104 (mp0) REVERT: C 53 MET cc_start: 0.8175 (tpt) cc_final: 0.7651 (tpt) REVERT: D 53 MET cc_start: 0.8032 (tpt) cc_final: 0.7670 (tpt) REVERT: D 92 ASP cc_start: 0.8549 (m-30) cc_final: 0.8287 (m-30) REVERT: E 53 MET cc_start: 0.8222 (tpt) cc_final: 0.7722 (tpt) REVERT: F 18 GLU cc_start: 0.7776 (mp0) cc_final: 0.7109 (mp0) REVERT: F 53 MET cc_start: 0.8146 (tpt) cc_final: 0.7622 (tpt) REVERT: a 1 MET cc_start: 0.6242 (mpp) cc_final: 0.5857 (mtp) REVERT: a 169 ASP cc_start: 0.8668 (m-30) cc_final: 0.8461 (m-30) REVERT: b 62 MET cc_start: 0.8179 (ttm) cc_final: 0.6591 (tpt) REVERT: b 118 GLN cc_start: 0.8984 (tp-100) cc_final: 0.6936 (pm20) REVERT: d 1 MET cc_start: 0.6260 (mpp) cc_final: 0.5865 (mtp) REVERT: d 169 ASP cc_start: 0.8646 (m-30) cc_final: 0.8437 (m-30) REVERT: e 62 MET cc_start: 0.8174 (ttm) cc_final: 0.6591 (tpt) REVERT: e 118 GLN cc_start: 0.8983 (tp-100) cc_final: 0.6936 (pm20) outliers start: 57 outliers final: 38 residues processed: 273 average time/residue: 0.1400 time to fit residues: 57.6452 Evaluate side-chains 257 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 76 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 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 76 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 237 GLU Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 158 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 48 optimal weight: 0.0020 chunk 181 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 149 optimal weight: 0.0170 overall best weight: 2.8032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.073791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065179 restraints weight = 61893.387| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.34 r_work: 0.3055 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18174 Z= 0.124 Angle : 0.554 7.297 24774 Z= 0.277 Chirality : 0.048 0.180 2922 Planarity : 0.004 0.042 3174 Dihedral : 4.217 21.400 2390 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.97 % Allowed : 21.02 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.19), residues: 2202 helix: 1.09 (0.31), residues: 258 sheet: 0.13 (0.24), residues: 444 loop : -0.18 (0.18), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 78 TYR 0.019 0.001 TYR E 120 PHE 0.007 0.001 PHE c 78 TRP 0.004 0.001 TRP D 90 HIS 0.003 0.001 HIS f 14 Details of bonding type rmsd covalent geometry : bond 0.00297 (18174) covalent geometry : angle 0.55383 (24774) hydrogen bonds : bond 0.03367 ( 396) hydrogen bonds : angle 5.26491 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7776 (mp0) cc_final: 0.7223 (mp0) REVERT: A 53 MET cc_start: 0.7992 (tpt) cc_final: 0.7644 (tpt) REVERT: A 92 ASP cc_start: 0.8531 (m-30) cc_final: 0.8290 (m-30) REVERT: B 18 GLU cc_start: 0.7713 (mp0) cc_final: 0.7093 (mp0) REVERT: B 53 MET cc_start: 0.8213 (tpt) cc_final: 0.7742 (tpt) REVERT: C 53 MET cc_start: 0.8151 (tpt) cc_final: 0.7673 (tpt) REVERT: D 18 GLU cc_start: 0.7777 (mp0) cc_final: 0.7224 (mp0) REVERT: D 53 MET cc_start: 0.7993 (tpt) cc_final: 0.7630 (tpt) REVERT: D 92 ASP cc_start: 0.8522 (m-30) cc_final: 0.8282 (m-30) REVERT: E 18 GLU cc_start: 0.7730 (mp0) cc_final: 0.7115 (mp0) REVERT: E 53 MET cc_start: 0.8231 (tpt) cc_final: 0.7757 (tpt) REVERT: F 53 MET cc_start: 0.8136 (tpt) cc_final: 0.7662 (tpt) REVERT: a 1 MET cc_start: 0.6120 (mpp) cc_final: 0.5733 (mtp) REVERT: a 169 ASP cc_start: 0.8674 (m-30) cc_final: 0.8467 (m-30) REVERT: b 1 MET cc_start: 0.6320 (mpp) cc_final: 0.6118 (mtt) REVERT: b 62 MET cc_start: 0.8257 (ttm) cc_final: 0.6718 (tpt) REVERT: b 118 GLN cc_start: 0.8996 (tp-100) cc_final: 0.6953 (pm20) REVERT: b 163 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8540 (mt-10) REVERT: c 62 MET cc_start: 0.7946 (mtp) cc_final: 0.6670 (tpt) REVERT: d 1 MET cc_start: 0.6143 (mpp) cc_final: 0.5746 (mtp) REVERT: d 169 ASP cc_start: 0.8647 (m-30) cc_final: 0.8437 (m-30) REVERT: e 62 MET cc_start: 0.8254 (ttm) cc_final: 0.6708 (tpt) REVERT: e 118 GLN cc_start: 0.9008 (tp-100) cc_final: 0.7031 (pm20) REVERT: e 163 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: f 62 MET cc_start: 0.7932 (mtp) cc_final: 0.6652 (tpt) outliers start: 62 outliers final: 38 residues processed: 281 average time/residue: 0.1309 time to fit residues: 55.2403 Evaluate side-chains 257 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain 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 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain 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 230 LEU Chi-restraints excluded: chain a residue 237 GLU Chi-restraints excluded: chain b residue 163 GLU Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 237 GLU Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 168 optimal weight: 20.0000 chunk 137 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.063713 restraints weight = 62953.209| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.32 r_work: 0.3019 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18174 Z= 0.163 Angle : 0.581 7.411 24774 Z= 0.289 Chirality : 0.048 0.215 2922 Planarity : 0.004 0.042 3174 Dihedral : 4.276 22.444 2390 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.26 % Allowed : 21.26 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.19), residues: 2202 helix: 1.02 (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 ARG 0.004 0.000 ARG E 78 TYR 0.023 0.001 TYR B 120 PHE 0.010 0.001 PHE E 85 TRP 0.006 0.001 TRP C 90 HIS 0.004 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00391 (18174) covalent geometry : angle 0.58077 (24774) hydrogen bonds : bond 0.03610 ( 396) hydrogen bonds : angle 5.28435 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8088 (tpt) cc_final: 0.7781 (tpt) REVERT: A 92 ASP cc_start: 0.8531 (m-30) cc_final: 0.8292 (m-30) REVERT: B 37 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8746 (mt) REVERT: B 53 MET cc_start: 0.8260 (tpt) cc_final: 0.7810 (tpt) REVERT: B 118 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8986 (pt) REVERT: C 18 GLU cc_start: 0.7670 (mp0) cc_final: 0.7026 (mp0) REVERT: C 53 MET cc_start: 0.8175 (tpt) cc_final: 0.7728 (tpt) REVERT: D 53 MET cc_start: 0.8103 (tpt) cc_final: 0.7800 (tpt) REVERT: D 92 ASP cc_start: 0.8539 (m-30) cc_final: 0.8299 (m-30) REVERT: E 37 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8752 (mt) REVERT: E 53 MET cc_start: 0.8257 (tpt) cc_final: 0.7804 (tpt) REVERT: E 118 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8984 (pt) REVERT: F 18 GLU cc_start: 0.7669 (mp0) cc_final: 0.7023 (mp0) REVERT: F 53 MET cc_start: 0.8170 (tpt) cc_final: 0.7720 (tpt) REVERT: b 118 GLN cc_start: 0.9017 (tp-100) cc_final: 0.7202 (pm20) REVERT: b 163 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8482 (mt-10) REVERT: c 62 MET cc_start: 0.7827 (mtp) cc_final: 0.6801 (tpt) REVERT: e 118 GLN cc_start: 0.9035 (tp-100) cc_final: 0.7224 (pm20) REVERT: e 163 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8527 (mt-10) REVERT: f 62 MET cc_start: 0.7809 (mtp) cc_final: 0.6778 (tpt) outliers start: 68 outliers final: 40 residues processed: 286 average time/residue: 0.1350 time to fit residues: 58.9161 Evaluate side-chains 262 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 118 LEU 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 230 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 163 GLU Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 66 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062678 restraints weight = 62767.472| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.32 r_work: 0.2995 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18174 Z= 0.191 Angle : 0.608 8.163 24774 Z= 0.303 Chirality : 0.049 0.203 2922 Planarity : 0.004 0.040 3174 Dihedral : 4.425 23.769 2390 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.92 % Allowed : 22.41 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.19), residues: 2202 helix: 0.91 (0.31), residues: 258 sheet: -0.49 (0.21), residues: 516 loop : -0.13 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 78 TYR 0.029 0.001 TYR E 120 PHE 0.010 0.001 PHE e 78 TRP 0.006 0.001 TRP D 90 HIS 0.005 0.001 HIS f 14 Details of bonding type rmsd covalent geometry : bond 0.00459 (18174) covalent geometry : angle 0.60751 (24774) hydrogen bonds : bond 0.03766 ( 396) hydrogen bonds : angle 5.27585 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.641 Fit side-chains REVERT: A 18 GLU cc_start: 0.7711 (mp0) cc_final: 0.7132 (mp0) REVERT: A 53 MET cc_start: 0.8108 (tpt) cc_final: 0.7835 (tpt) REVERT: A 92 ASP cc_start: 0.8540 (m-30) cc_final: 0.8291 (m-30) REVERT: B 18 GLU cc_start: 0.7727 (mp0) cc_final: 0.7110 (mp0) REVERT: B 32 TYR cc_start: 0.8227 (t80) cc_final: 0.7970 (t80) REVERT: B 37 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8750 (mt) REVERT: B 53 MET cc_start: 0.8304 (tpt) cc_final: 0.7931 (tpt) REVERT: B 118 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8935 (pt) REVERT: C 53 MET cc_start: 0.8241 (tpt) cc_final: 0.7802 (tpt) REVERT: D 18 GLU cc_start: 0.7701 (mp0) cc_final: 0.7114 (mp0) REVERT: D 53 MET cc_start: 0.8107 (tpt) cc_final: 0.7833 (tpt) REVERT: D 92 ASP cc_start: 0.8539 (m-30) cc_final: 0.8288 (m-30) REVERT: E 18 GLU cc_start: 0.7739 (mp0) cc_final: 0.7120 (mp0) REVERT: E 32 TYR cc_start: 0.8242 (t80) cc_final: 0.7982 (t80) REVERT: E 37 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8752 (mt) REVERT: E 53 MET cc_start: 0.8324 (tpt) cc_final: 0.7946 (tpt) REVERT: E 118 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8946 (pt) REVERT: F 53 MET cc_start: 0.8223 (tpt) cc_final: 0.7786 (tpt) REVERT: b 118 GLN cc_start: 0.9106 (tp-100) cc_final: 0.7221 (pm20) REVERT: b 163 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8518 (mt-10) REVERT: c 62 MET cc_start: 0.8153 (mtp) cc_final: 0.6889 (tpt) REVERT: e 118 GLN cc_start: 0.9113 (tp-100) cc_final: 0.7234 (pm20) REVERT: e 163 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8504 (mt-10) REVERT: f 62 MET cc_start: 0.8146 (mtp) cc_final: 0.6877 (tpt) outliers start: 61 outliers final: 38 residues processed: 266 average time/residue: 0.1349 time to fit residues: 54.0994 Evaluate side-chains 254 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 118 LEU 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 230 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 163 GLU Chi-restraints excluded: chain b residue 193 ILE Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 193 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 109 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 188 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.0170 chunk 9 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063089 restraints weight = 62644.872| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.41 r_work: 0.3002 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18174 Z= 0.150 Angle : 0.589 8.041 24774 Z= 0.294 Chirality : 0.049 0.197 2922 Planarity : 0.004 0.040 3174 Dihedral : 4.401 23.432 2390 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.25 % Allowed : 22.84 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.19), residues: 2202 helix: 0.90 (0.31), residues: 258 sheet: -0.52 (0.21), residues: 516 loop : -0.16 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.036 0.001 TYR E 120 PHE 0.007 0.001 PHE c 171 TRP 0.005 0.001 TRP D 90 HIS 0.003 0.001 HIS d 14 Details of bonding type rmsd covalent geometry : bond 0.00363 (18174) covalent geometry : angle 0.58878 (24774) hydrogen bonds : bond 0.03548 ( 396) hydrogen bonds : angle 5.28454 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.667 Fit side-chains REVERT: A 18 GLU cc_start: 0.7719 (mp0) cc_final: 0.7116 (mp0) REVERT: A 53 MET cc_start: 0.8109 (tpt) cc_final: 0.7822 (tpt) REVERT: B 18 GLU cc_start: 0.7757 (mp0) cc_final: 0.7142 (mp0) REVERT: B 32 TYR cc_start: 0.8146 (t80) cc_final: 0.7899 (t80) REVERT: B 53 MET cc_start: 0.8282 (tpt) cc_final: 0.7920 (tpt) REVERT: B 118 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8868 (pt) REVERT: C 18 GLU cc_start: 0.7832 (mp0) cc_final: 0.7047 (mp0) REVERT: C 53 MET cc_start: 0.8166 (tpt) cc_final: 0.7755 (tpt) REVERT: D 18 GLU cc_start: 0.7719 (mp0) cc_final: 0.7115 (mp0) REVERT: D 53 MET cc_start: 0.8103 (tpt) cc_final: 0.7817 (tpt) REVERT: E 18 GLU cc_start: 0.7770 (mp0) cc_final: 0.7155 (mp0) REVERT: E 32 TYR cc_start: 0.8162 (t80) cc_final: 0.7913 (t80) REVERT: E 53 MET cc_start: 0.8255 (tpt) cc_final: 0.7883 (tpt) REVERT: E 118 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8872 (pt) REVERT: F 18 GLU cc_start: 0.7832 (mp0) cc_final: 0.7051 (mp0) REVERT: F 53 MET cc_start: 0.8144 (tpt) cc_final: 0.7731 (tpt) REVERT: b 1 MET cc_start: 0.6349 (mpp) cc_final: 0.6131 (mtt) REVERT: b 118 GLN cc_start: 0.9051 (tp-100) cc_final: 0.7203 (pm20) REVERT: b 163 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: c 62 MET cc_start: 0.8117 (mtp) cc_final: 0.6857 (tpt) REVERT: c 118 GLN cc_start: 0.9096 (tp-100) cc_final: 0.7151 (pm20) REVERT: e 1 MET cc_start: 0.6215 (mpp) cc_final: 0.5875 (mtt) REVERT: e 118 GLN cc_start: 0.9061 (tp-100) cc_final: 0.7203 (pm20) REVERT: e 163 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8511 (mt-10) REVERT: f 62 MET cc_start: 0.8096 (mtp) cc_final: 0.6847 (tpt) REVERT: f 118 GLN cc_start: 0.9086 (tp-100) cc_final: 0.7147 (pm20) outliers start: 47 outliers final: 38 residues processed: 252 average time/residue: 0.1207 time to fit residues: 45.9984 Evaluate side-chains 251 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 118 LEU 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 230 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 163 GLU Chi-restraints excluded: chain b residue 193 ILE Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 193 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 111 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.063394 restraints weight = 62525.789| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.38 r_work: 0.3013 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18174 Z= 0.141 Angle : 0.583 7.700 24774 Z= 0.291 Chirality : 0.048 0.186 2922 Planarity : 0.004 0.040 3174 Dihedral : 4.368 27.267 2390 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.20 % Allowed : 23.04 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.19), residues: 2202 helix: 0.91 (0.31), residues: 258 sheet: -0.56 (0.21), residues: 516 loop : -0.16 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 78 TYR 0.031 0.001 TYR B 120 PHE 0.007 0.001 PHE c 171 TRP 0.005 0.001 TRP E 90 HIS 0.003 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00343 (18174) covalent geometry : angle 0.58283 (24774) hydrogen bonds : bond 0.03423 ( 396) hydrogen bonds : angle 5.19563 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4404 Ramachandran restraints generated. 2202 Oldfield, 0 Emsley, 2202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 207 time to evaluate : 0.693 Fit side-chains REVERT: A 18 GLU cc_start: 0.7736 (mp0) cc_final: 0.7186 (mp0) REVERT: A 53 MET cc_start: 0.8117 (tpt) cc_final: 0.7836 (tpt) REVERT: B 18 GLU cc_start: 0.7700 (mp0) cc_final: 0.7096 (mp0) REVERT: B 32 TYR cc_start: 0.8186 (t80) cc_final: 0.7891 (t80) REVERT: B 53 MET cc_start: 0.8322 (tpt) cc_final: 0.7948 (tpt) REVERT: B 118 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8876 (pt) REVERT: C 18 GLU cc_start: 0.7705 (mp0) cc_final: 0.6827 (mp0) REVERT: C 53 MET cc_start: 0.8156 (tpt) cc_final: 0.7777 (tpt) REVERT: D 18 GLU cc_start: 0.7721 (mp0) cc_final: 0.7164 (mp0) REVERT: D 53 MET cc_start: 0.8097 (tpt) cc_final: 0.7813 (tpt) REVERT: E 18 GLU cc_start: 0.7703 (mp0) cc_final: 0.7099 (mp0) REVERT: E 32 TYR cc_start: 0.8195 (t80) cc_final: 0.7900 (t80) REVERT: E 53 MET cc_start: 0.8327 (tpt) cc_final: 0.7964 (tpt) REVERT: E 118 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8871 (pt) REVERT: F 18 GLU cc_start: 0.7692 (mp0) cc_final: 0.6805 (mp0) REVERT: F 53 MET cc_start: 0.8140 (tpt) cc_final: 0.7763 (tpt) REVERT: b 1 MET cc_start: 0.6395 (mpp) cc_final: 0.6149 (mtt) REVERT: b 62 MET cc_start: 0.8332 (ttm) cc_final: 0.6771 (tpt) REVERT: b 118 GLN cc_start: 0.9018 (tp-100) cc_final: 0.7172 (pm20) REVERT: c 62 MET cc_start: 0.8109 (mtp) cc_final: 0.6832 (tpt) REVERT: c 118 GLN cc_start: 0.9080 (tp-100) cc_final: 0.7131 (pm20) REVERT: e 1 MET cc_start: 0.6088 (mpp) cc_final: 0.5884 (mtt) REVERT: e 62 MET cc_start: 0.8331 (ttm) cc_final: 0.6768 (tpt) REVERT: e 118 GLN cc_start: 0.9030 (tp-100) cc_final: 0.7184 (pm20) REVERT: e 163 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: f 62 MET cc_start: 0.8100 (mtp) cc_final: 0.6827 (tpt) REVERT: f 118 GLN cc_start: 0.9070 (tp-100) cc_final: 0.7125 (pm20) outliers start: 46 outliers final: 36 residues processed: 245 average time/residue: 0.1214 time to fit residues: 45.0398 Evaluate side-chains 243 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU 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 76 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 118 LEU 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 230 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 193 ILE Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 82 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 163 GLU Chi-restraints excluded: chain e residue 193 ILE Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 82 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 153 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 205 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.062689 restraints weight = 62850.352| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.38 r_work: 0.2990 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18174 Z= 0.166 Angle : 0.603 8.726 24774 Z= 0.299 Chirality : 0.048 0.185 2922 Planarity : 0.005 0.072 3174 Dihedral : 4.456 28.496 2390 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.16 % Allowed : 22.70 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.19), residues: 2202 helix: 0.85 (0.31), residues: 258 sheet: -0.62 (0.21), residues: 516 loop : -0.16 (0.19), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 128 TYR 0.030 0.001 TYR E 120 PHE 0.011 0.001 PHE B 85 TRP 0.005 0.001 TRP B 90 HIS 0.005 0.001 HIS d 14 Details of bonding type rmsd covalent geometry : bond 0.00401 (18174) covalent geometry : angle 0.60273 (24774) hydrogen bonds : bond 0.03499 ( 396) hydrogen bonds : angle 5.20288 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.28 seconds wall clock time: 52 minutes 20.85 seconds (3140.85 seconds total)