Starting phenix.real_space_refine on Mon Aug 25 07:53:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8heg_34690/08_2025/8heg_34690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8heg_34690/08_2025/8heg_34690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8heg_34690/08_2025/8heg_34690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8heg_34690/08_2025/8heg_34690.map" model { file = "/net/cci-nas-00/data/ceres_data/8heg_34690/08_2025/8heg_34690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8heg_34690/08_2025/8heg_34690.cif" } resolution = 3.2 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= 0.004 sd= 0.131 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 105 5.16 5 C 16940 2.51 5 N 4615 2.21 5 O 4935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.03s 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: 26595 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "B" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Restraints were copied for chains: E, I, M, Q, F, J, N, R, G, K, O, S, H, L, P, T Time building chain proxies: 4.12, per 1000 atoms: 0.15 Number of scatterers: 26595 At special positions: 0 Unit cell: (180.83, 181.9, 93.09, 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 105 16.00 O 4935 8.00 N 4615 7.00 C 16940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 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=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 973.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6300 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 65 sheets defined 13.1% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR A 56 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER A 99 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 59' Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.548A pdb=" N HIS B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR B 138 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 140 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR B 141 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 142 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.644A pdb=" N VAL C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 4.546A pdb=" N ASN C 88 " --> pdb=" O HIS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.503A pdb=" N TYR D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR E 56 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU F 59 " --> pdb=" O THR F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 59' Processing helix chain 'F' and resid 89 through 97 removed outlier: 3.548A pdb=" N HIS F 93 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR F 138 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU F 140 " --> pdb=" O LYS F 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR F 141 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 142 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE F 143 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 51 removed outlier: 3.644A pdb=" N VAL G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 88 removed outlier: 4.546A pdb=" N ASN G 88 " --> pdb=" O HIS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 138 through 143 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.504A pdb=" N TYR H 31 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET I 36 " --> pdb=" O VAL I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR I 56 " --> pdb=" O LEU I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 68 Processing helix chain 'I' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER I 99 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN I 100 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU J 59 " --> pdb=" O THR J 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 59' Processing helix chain 'J' and resid 89 through 97 removed outlier: 3.549A pdb=" N HIS J 93 " --> pdb=" O GLY J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR J 138 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU J 140 " --> pdb=" O LYS J 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR J 141 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU J 142 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 51 removed outlier: 3.643A pdb=" N VAL K 47 " --> pdb=" O ASN K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 88 removed outlier: 4.546A pdb=" N ASN K 88 " --> pdb=" O HIS K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 96 Processing helix chain 'K' and resid 138 through 143 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.503A pdb=" N TYR L 31 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR L 32 " --> pdb=" O PHE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 28 through 32' Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'M' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET M 36 " --> pdb=" O VAL M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR M 56 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER M 99 " --> pdb=" O ALA M 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN M 100 " --> pdb=" O ALA M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU N 59 " --> pdb=" O THR N 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 59' Processing helix chain 'N' and resid 89 through 97 removed outlier: 3.548A pdb=" N HIS N 93 " --> pdb=" O GLY N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR N 138 " --> pdb=" O ARG N 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU N 140 " --> pdb=" O LYS N 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR N 141 " --> pdb=" O TYR N 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU N 142 " --> pdb=" O GLN N 139 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE N 143 " --> pdb=" O LEU N 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 51 removed outlier: 3.644A pdb=" N VAL O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 88 removed outlier: 4.546A pdb=" N ASN O 88 " --> pdb=" O HIS O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 96 Processing helix chain 'O' and resid 138 through 143 Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.503A pdb=" N TYR P 31 " --> pdb=" O ALA P 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR P 32 " --> pdb=" O PHE P 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 28 through 32' Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'Q' and resid 31 through 36 removed outlier: 3.616A pdb=" N MET Q 36 " --> pdb=" O VAL Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 56 removed outlier: 3.645A pdb=" N THR Q 56 " --> pdb=" O LEU Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 68 Processing helix chain 'Q' and resid 94 through 100 removed outlier: 3.596A pdb=" N SER Q 99 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN Q 100 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 59 removed outlier: 3.802A pdb=" N GLU R 59 " --> pdb=" O THR R 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 56 through 59' Processing helix chain 'R' and resid 89 through 97 removed outlier: 3.548A pdb=" N HIS R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 143 removed outlier: 3.596A pdb=" N TYR R 138 " --> pdb=" O ARG R 135 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU R 140 " --> pdb=" O LYS R 137 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR R 141 " --> pdb=" O TYR R 138 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU R 142 " --> pdb=" O GLN R 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE R 143 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 51 removed outlier: 3.643A pdb=" N VAL S 47 " --> pdb=" O ASN S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 88 removed outlier: 4.547A pdb=" N ASN S 88 " --> pdb=" O HIS S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 96 Processing helix chain 'S' and resid 138 through 143 Processing helix chain 'T' and resid 28 through 32 removed outlier: 3.503A pdb=" N TYR T 31 " --> pdb=" O ALA T 28 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR T 32 " --> pdb=" O PHE T 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 28 through 32' Processing helix chain 'T' and resid 87 through 91 Processing sheet with id=1, first strand: chain 'A' and resid 40 through 41 removed outlier: 4.321A pdb=" N ASP A 171 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 83 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG A 81 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU A 175 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 79 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL A 177 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 77 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=3, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR A 72 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR A 185 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR A 72 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU A 183 " --> pdb=" O TYR A 72 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.912A pdb=" N TYR B 100 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU B 213 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE B 98 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 68 through 69 removed outlier: 4.120A pdb=" N LYS B 198 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 78 through 82 removed outlier: 6.489A pdb=" N CYS B 120 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY B 118 " --> pdb=" O PRO B 186 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.587A pdb=" N ILE B 158 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.543A pdb=" N THR C 53 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU C 73 " --> pdb=" O GLN C 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN C 189 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 75 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY C 183 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG C 120 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 144 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=11, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=12, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER D 121 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 12 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER D 121 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 12 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 111 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'E' and resid 40 through 41 removed outlier: 4.322A pdb=" N ASP E 171 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 83 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG E 81 " --> pdb=" O SER E 173 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU E 175 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL E 79 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL E 177 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU E 77 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=16, first strand: chain 'E' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR E 72 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR E 185 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR E 72 " --> pdb=" O GLU E 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU E 183 " --> pdb=" O TYR E 72 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.911A pdb=" N TYR F 100 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU F 213 " --> pdb=" O PHE F 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE F 98 " --> pdb=" O GLU F 213 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'F' and resid 68 through 69 removed outlier: 4.121A pdb=" N LYS F 198 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'F' and resid 78 through 82 removed outlier: 6.490A pdb=" N CYS F 120 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY F 118 " --> pdb=" O PRO F 186 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'F' and resid 158 through 160 removed outlier: 3.587A pdb=" N ILE F 158 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.543A pdb=" N THR G 53 " --> pdb=" O VAL G 204 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'G' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU G 73 " --> pdb=" O GLN G 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN G 189 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA G 75 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY G 183 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG G 120 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE G 144 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'G' and resid 100 through 101 Processing sheet with id=24, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=25, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER H 121 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL H 12 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY H 10 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER H 121 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL H 12 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR H 111 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'I' and resid 40 through 41 removed outlier: 4.321A pdb=" N ASP I 171 " --> pdb=" O GLU I 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU I 83 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG I 81 " --> pdb=" O SER I 173 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU I 175 " --> pdb=" O VAL I 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL I 79 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL I 177 " --> pdb=" O GLU I 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU I 77 " --> pdb=" O VAL I 177 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=29, first strand: chain 'I' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR I 72 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR I 185 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR I 72 " --> pdb=" O GLU I 183 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU I 183 " --> pdb=" O TYR I 72 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.911A pdb=" N TYR J 100 " --> pdb=" O ALA J 211 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU J 213 " --> pdb=" O PHE J 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE J 98 " --> pdb=" O GLU J 213 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'J' and resid 68 through 69 removed outlier: 4.121A pdb=" N LYS J 198 " --> pdb=" O VAL J 112 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'J' and resid 78 through 82 removed outlier: 6.489A pdb=" N CYS J 120 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY J 118 " --> pdb=" O PRO J 186 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'J' and resid 158 through 160 removed outlier: 3.588A pdb=" N ILE J 158 " --> pdb=" O VAL J 107 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.543A pdb=" N THR K 53 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'K' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU K 73 " --> pdb=" O GLN K 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN K 189 " --> pdb=" O LEU K 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA K 75 " --> pdb=" O ILE K 187 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY K 183 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG K 120 " --> pdb=" O ILE K 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE K 144 " --> pdb=" O TYR K 125 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=37, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=38, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.323A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER L 121 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL L 12 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA L 50 " --> pdb=" O MET L 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.323A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER L 121 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL L 12 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR L 111 " --> pdb=" O GLY L 98 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'M' and resid 40 through 41 removed outlier: 4.322A pdb=" N ASP M 171 " --> pdb=" O GLU M 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU M 83 " --> pdb=" O ASP M 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG M 81 " --> pdb=" O SER M 173 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU M 175 " --> pdb=" O VAL M 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL M 79 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL M 177 " --> pdb=" O GLU M 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU M 77 " --> pdb=" O VAL M 177 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'M' and resid 48 through 50 Processing sheet with id=42, first strand: chain 'M' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR M 72 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR M 185 " --> pdb=" O THR M 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR M 72 " --> pdb=" O GLU M 183 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU M 183 " --> pdb=" O TYR M 72 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'N' and resid 53 through 54 removed outlier: 3.912A pdb=" N TYR N 100 " --> pdb=" O ALA N 211 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLU N 213 " --> pdb=" O PHE N 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE N 98 " --> pdb=" O GLU N 213 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'N' and resid 68 through 69 removed outlier: 4.121A pdb=" N LYS N 198 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'N' and resid 78 through 82 removed outlier: 6.489A pdb=" N CYS N 120 " --> pdb=" O VAL N 184 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY N 118 " --> pdb=" O PRO N 186 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'N' and resid 158 through 160 removed outlier: 3.587A pdb=" N ILE N 158 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 53 through 54 removed outlier: 3.543A pdb=" N THR O 53 " --> pdb=" O VAL O 204 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU O 73 " --> pdb=" O GLN O 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN O 189 " --> pdb=" O LEU O 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA O 75 " --> pdb=" O ILE O 187 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY O 183 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG O 120 " --> pdb=" O ILE O 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE O 144 " --> pdb=" O TYR O 125 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=50, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=51, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY P 10 " --> pdb=" O THR P 119 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER P 121 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL P 12 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N MET P 34 " --> pdb=" O ALA P 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY P 10 " --> pdb=" O THR P 119 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER P 121 " --> pdb=" O GLY P 10 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL P 12 " --> pdb=" O SER P 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR P 111 " --> pdb=" O GLY P 98 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'Q' and resid 40 through 41 removed outlier: 4.321A pdb=" N ASP Q 171 " --> pdb=" O GLU Q 83 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU Q 83 " --> pdb=" O ASP Q 171 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ARG Q 81 " --> pdb=" O SER Q 173 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU Q 175 " --> pdb=" O VAL Q 79 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL Q 79 " --> pdb=" O LEU Q 175 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL Q 177 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU Q 77 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'Q' and resid 48 through 50 Processing sheet with id=55, first strand: chain 'Q' and resid 126 through 127 removed outlier: 3.563A pdb=" N TYR Q 72 " --> pdb=" O LEU Q 126 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR Q 185 " --> pdb=" O THR Q 70 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR Q 72 " --> pdb=" O GLU Q 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU Q 183 " --> pdb=" O TYR Q 72 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'R' and resid 53 through 54 removed outlier: 3.912A pdb=" N TYR R 100 " --> pdb=" O ALA R 211 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLU R 213 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE R 98 " --> pdb=" O GLU R 213 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'R' and resid 68 through 69 removed outlier: 4.120A pdb=" N LYS R 198 " --> pdb=" O VAL R 112 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'R' and resid 78 through 82 removed outlier: 6.490A pdb=" N CYS R 120 " --> pdb=" O VAL R 184 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLY R 118 " --> pdb=" O PRO R 186 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'R' and resid 158 through 160 removed outlier: 3.587A pdb=" N ILE R 158 " --> pdb=" O VAL R 107 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'S' and resid 53 through 54 removed outlier: 3.544A pdb=" N THR S 53 " --> pdb=" O VAL S 204 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'S' and resid 73 through 79 removed outlier: 6.736A pdb=" N LEU S 73 " --> pdb=" O GLN S 189 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN S 189 " --> pdb=" O LEU S 73 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA S 75 " --> pdb=" O ILE S 187 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY S 183 " --> pdb=" O VAL S 79 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG S 120 " --> pdb=" O ILE S 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE S 144 " --> pdb=" O TYR S 125 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'S' and resid 100 through 101 Processing sheet with id=63, first strand: chain 'T' and resid 3 through 7 Processing sheet with id=64, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY T 10 " --> pdb=" O THR T 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER T 121 " --> pdb=" O GLY T 10 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL T 12 " --> pdb=" O SER T 121 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N MET T 34 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA T 50 " --> pdb=" O MET T 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.322A pdb=" N GLY T 10 " --> pdb=" O THR T 119 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N SER T 121 " --> pdb=" O GLY T 10 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL T 12 " --> pdb=" O SER T 121 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR T 111 " --> pdb=" O GLY T 98 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 1665 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: 5.09 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6610 1.33 - 1.45: 5771 1.45 - 1.57: 14759 1.57 - 1.69: 5 1.69 - 1.81: 165 Bond restraints: 27310 Sorted by residual: bond pdb=" CA TYR F 200 " pdb=" C TYR F 200 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.24e+01 bond pdb=" CA TYR J 200 " pdb=" C TYR J 200 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.22e+01 bond pdb=" CA TYR B 200 " pdb=" C TYR B 200 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.20e+01 bond pdb=" CA TYR R 200 " pdb=" C TYR R 200 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.20e+01 bond pdb=" CA TYR N 200 " pdb=" C TYR N 200 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.18e+01 ... (remaining 27305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 36331 2.12 - 4.23: 799 4.23 - 6.35: 55 6.35 - 8.46: 5 8.46 - 10.58: 5 Bond angle restraints: 37195 Sorted by residual: angle pdb=" CA PRO S 62 " pdb=" N PRO S 62 " pdb=" CD PRO S 62 " ideal model delta sigma weight residual 112.00 101.42 10.58 1.40e+00 5.10e-01 5.71e+01 angle pdb=" CA PRO O 62 " pdb=" N PRO O 62 " pdb=" CD PRO O 62 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 angle pdb=" CA PRO C 62 " pdb=" N PRO C 62 " pdb=" CD PRO C 62 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 angle pdb=" CA PRO K 62 " pdb=" N PRO K 62 " pdb=" CD PRO K 62 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 angle pdb=" CA PRO G 62 " pdb=" N PRO G 62 " pdb=" CD PRO G 62 " ideal model delta sigma weight residual 112.00 101.44 10.56 1.40e+00 5.10e-01 5.69e+01 ... (remaining 37190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 13996 17.81 - 35.63: 1675 35.63 - 53.44: 336 53.44 - 71.26: 58 71.26 - 89.07: 25 Dihedral angle restraints: 16090 sinusoidal: 6245 harmonic: 9845 Sorted by residual: dihedral pdb=" CA LEU K 212 " pdb=" C LEU K 212 " pdb=" N ARG K 213 " pdb=" CA ARG K 213 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU C 212 " pdb=" C LEU C 212 " pdb=" N ARG C 213 " pdb=" CA ARG C 213 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU G 212 " pdb=" C LEU G 212 " pdb=" N ARG G 213 " pdb=" CA ARG G 213 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 16087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2507 0.032 - 0.065: 1033 0.065 - 0.097: 356 0.097 - 0.129: 158 0.129 - 0.161: 26 Chirality restraints: 4080 Sorted by residual: chirality pdb=" CA TYR J 200 " pdb=" N TYR J 200 " pdb=" C TYR J 200 " pdb=" CB TYR J 200 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA TYR R 200 " pdb=" N TYR R 200 " pdb=" C TYR R 200 " pdb=" CB TYR R 200 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA TYR N 200 " pdb=" N TYR N 200 " pdb=" C TYR N 200 " pdb=" CB TYR N 200 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 4077 not shown) Planarity restraints: 4795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 61 " 0.059 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO G 62 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO G 62 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 62 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 61 " 0.059 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO K 62 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO K 62 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO K 62 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 61 " -0.059 5.00e-02 4.00e+02 8.35e-02 1.11e+01 pdb=" N PRO C 62 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " -0.046 5.00e-02 4.00e+02 ... (remaining 4792 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.42: 130 1.42 - 2.29: 335 2.29 - 3.16: 21202 3.16 - 4.03: 63226 4.03 - 4.90: 123070 Warning: very small nonbonded interaction distances. Nonbonded interactions: 207963 Sorted by model distance: nonbonded pdb=" CD LYS C 28 " pdb=" CD2 HIS I 28 " model vdw 0.548 3.660 nonbonded pdb=" CD2 HIS E 28 " pdb=" CD LYS S 28 " model vdw 0.548 3.660 nonbonded pdb=" CD2 HIS A 28 " pdb=" CD LYS O 28 " model vdw 0.548 3.660 nonbonded pdb=" CD LYS G 28 " pdb=" CD2 HIS M 28 " model vdw 0.548 3.660 nonbonded pdb=" CD LYS K 28 " pdb=" CD2 HIS Q 28 " model vdw 0.548 3.660 ... (remaining 207958 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' } 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: 1.470 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 21.670 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 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 : 0.030 1.027 27345 Z= 3.029 Angle : 0.702 10.578 37205 Z= 0.419 Chirality : 0.044 0.161 4080 Planarity : 0.006 0.084 4795 Dihedral : 15.873 89.073 9775 Min Nonbonded Distance : 0.548 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.08 % Favored : 92.62 % Rotamer: Outliers : 1.09 % Allowed : 22.19 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.33 (0.14), residues: 3335 helix: -0.42 (0.39), residues: 160 sheet: -0.49 (0.17), residues: 1010 loop : -1.13 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 100 TYR 0.019 0.002 TYR L 60 PHE 0.014 0.002 PHE H 47 TRP 0.017 0.001 TRP K 148 HIS 0.002 0.001 HIS M 49 Details of bonding type rmsd covalent geometry : bond 0.00409 (27310) covalent geometry : angle 0.70251 (37195) SS BOND : bond 0.00037 ( 5) SS BOND : angle 0.22607 ( 10) hydrogen bonds : bond 0.26904 ( 710) hydrogen bonds : angle 9.08581 ( 1665) Misc. bond : bond 0.91244 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 357 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6974 (p90) REVERT: D 60 TYR cc_start: 0.7958 (m-80) cc_final: 0.7736 (m-80) REVERT: F 62 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6732 (p90) REVERT: J 59 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6775 (mt-10) REVERT: J 62 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6083 (p90) REVERT: K 184 TRP cc_start: 0.3501 (m-10) cc_final: 0.3226 (m-10) REVERT: N 59 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6889 (mt-10) REVERT: O 84 LYS cc_start: 0.8153 (tttm) cc_final: 0.7572 (ttpp) REVERT: O 86 MET cc_start: 0.9111 (mmm) cc_final: 0.8767 (mmm) REVERT: Q 119 TYR cc_start: 0.8200 (t80) cc_final: 0.7919 (t80) REVERT: R 59 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6965 (mt-10) REVERT: R 62 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7125 (p90) REVERT: R 101 MET cc_start: 0.7800 (mtm) cc_final: 0.7411 (mtp) REVERT: R 196 GLU cc_start: 0.6689 (tt0) cc_final: 0.6437 (tt0) outliers start: 31 outliers final: 19 residues processed: 373 average time/residue: 0.1835 time to fit residues: 104.4622 Evaluate side-chains 348 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 325 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 62 PHE Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 62 PHE Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain T residue 58 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.0040 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS C 31 ASN C 145 HIS C 221 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 HIS K 31 ASN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 HIS O 31 ASN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 HIS S 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.211706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.166004 restraints weight = 29722.539| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 3.73 r_work: 0.3405 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 27345 Z= 0.219 Angle : 0.722 7.985 37205 Z= 0.388 Chirality : 0.048 0.430 4080 Planarity : 0.008 0.162 4795 Dihedral : 5.999 48.369 3759 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.69 % Favored : 93.01 % Rotamer: Outliers : 4.51 % Allowed : 19.40 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.35 (0.14), residues: 3335 helix: -0.36 (0.41), residues: 160 sheet: -0.27 (0.16), residues: 1035 loop : -1.30 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.002 ARG I 114 TYR 0.023 0.002 TYR K 30 PHE 0.015 0.002 PHE K 77 TRP 0.021 0.001 TRP S 148 HIS 0.025 0.002 HIS Q 29 Details of bonding type rmsd covalent geometry : bond 0.00518 (27310) covalent geometry : angle 0.72165 (37195) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.76069 ( 10) hydrogen bonds : bond 0.05128 ( 710) hydrogen bonds : angle 7.19848 ( 1665) Misc. bond : bond 0.00965 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 341 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 TYR cc_start: 0.8745 (m-10) cc_final: 0.7776 (m-10) REVERT: C 120 ARG cc_start: 0.6137 (mmt90) cc_final: 0.5817 (mmm-85) REVERT: C 145 HIS cc_start: 0.7159 (p90) cc_final: 0.6897 (p-80) REVERT: D 60 TYR cc_start: 0.7659 (m-80) cc_final: 0.7130 (m-80) REVERT: E 125 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8200 (m) REVERT: F 62 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6765 (p90) REVERT: G 34 ARG cc_start: 0.7844 (mmt180) cc_final: 0.7489 (mtm-85) REVERT: G 122 MET cc_start: 0.6890 (ptp) cc_final: 0.6485 (ptt) REVERT: G 145 HIS cc_start: 0.7160 (p-80) cc_final: 0.6866 (p-80) REVERT: I 125 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8242 (m) REVERT: J 62 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.5886 (p90) REVERT: K 86 MET cc_start: 0.8992 (mmm) cc_final: 0.8490 (mtp) REVERT: L 60 TYR cc_start: 0.7701 (m-80) cc_final: 0.7444 (m-80) REVERT: M 125 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8378 (m) REVERT: N 108 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7728 (mt-10) REVERT: O 34 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7547 (mtm-85) REVERT: O 86 MET cc_start: 0.8945 (mmm) cc_final: 0.8502 (mmm) REVERT: O 145 HIS cc_start: 0.7146 (p-80) cc_final: 0.6925 (p-80) REVERT: Q 119 TYR cc_start: 0.8311 (t80) cc_final: 0.7938 (t80) REVERT: Q 125 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8363 (m) REVERT: R 62 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6638 (p90) REVERT: R 101 MET cc_start: 0.8031 (mtm) cc_final: 0.7810 (mtp) REVERT: R 108 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7894 (mm-30) REVERT: R 182 MET cc_start: 0.9128 (ttp) cc_final: 0.8817 (ttm) REVERT: R 196 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6172 (tt0) REVERT: S 34 ARG cc_start: 0.7936 (mmt180) cc_final: 0.7405 (mtm-85) REVERT: S 120 ARG cc_start: 0.6247 (mmm-85) cc_final: 0.5940 (mmt90) REVERT: S 122 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6281 (ptt) outliers start: 128 outliers final: 69 residues processed: 427 average time/residue: 0.1832 time to fit residues: 119.4189 Evaluate side-chains 393 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 62 PHE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 62 PHE Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 62 PHE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 196 GLU Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 80 SER Chi-restraints excluded: chain S residue 122 MET Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 209 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 280 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** 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 = 0.4398 r_free = 0.4398 target = 0.213933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167226 restraints weight = 29563.412| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.65 r_work: 0.3408 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27345 Z= 0.132 Angle : 0.602 8.591 37205 Z= 0.323 Chirality : 0.045 0.367 4080 Planarity : 0.011 0.476 4795 Dihedral : 5.643 81.052 3750 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.72 % Favored : 93.13 % Rotamer: Outliers : 3.63 % Allowed : 20.07 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.16 (0.14), residues: 3335 helix: -0.29 (0.42), residues: 160 sheet: -0.09 (0.16), residues: 1070 loop : -1.21 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 200 TYR 0.020 0.001 TYR K 30 PHE 0.010 0.001 PHE E 73 TRP 0.013 0.001 TRP K 148 HIS 0.013 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00299 (27310) covalent geometry : angle 0.60201 (37195) SS BOND : bond 0.00164 ( 5) SS BOND : angle 0.69892 ( 10) hydrogen bonds : bond 0.03752 ( 710) hydrogen bonds : angle 6.54856 ( 1665) Misc. bond : bond 0.00886 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 318 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LYS cc_start: 0.7787 (mttm) cc_final: 0.7433 (mtpt) REVERT: C 107 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7942 (mp) REVERT: C 120 ARG cc_start: 0.6150 (mmt90) cc_final: 0.5941 (mmm-85) REVERT: D 60 TYR cc_start: 0.7658 (m-80) cc_final: 0.6947 (m-80) REVERT: E 54 MET cc_start: 0.8718 (tpp) cc_final: 0.8333 (mmm) REVERT: E 123 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.6896 (m90) REVERT: F 148 ILE cc_start: 0.8536 (mt) cc_final: 0.8328 (tt) REVERT: G 43 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8659 (t0) REVERT: G 76 LYS cc_start: 0.7562 (mttm) cc_final: 0.7214 (mtpt) REVERT: G 145 HIS cc_start: 0.7239 (p-80) cc_final: 0.6704 (p90) REVERT: G 198 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6929 (t70) REVERT: I 54 MET cc_start: 0.8716 (tpp) cc_final: 0.8397 (mmm) REVERT: I 125 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8282 (m) REVERT: M 123 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.6985 (m90) REVERT: O 76 LYS cc_start: 0.7682 (mttm) cc_final: 0.7379 (mtpt) REVERT: O 86 MET cc_start: 0.8853 (mmm) cc_final: 0.8382 (mmm) REVERT: O 145 HIS cc_start: 0.7234 (p-80) cc_final: 0.6997 (p-80) REVERT: Q 54 MET cc_start: 0.8745 (tpp) cc_final: 0.8457 (mmm) REVERT: Q 125 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8272 (m) REVERT: R 101 MET cc_start: 0.7871 (mtm) cc_final: 0.7274 (mtp) REVERT: S 34 ARG cc_start: 0.7691 (mmt180) cc_final: 0.7395 (mtm-85) REVERT: S 76 LYS cc_start: 0.7770 (mttm) cc_final: 0.7517 (mtpt) outliers start: 103 outliers final: 65 residues processed: 388 average time/residue: 0.1834 time to fit residues: 109.1062 Evaluate side-chains 370 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 146 GLN Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 125 VAL Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 239 optimal weight: 0.9990 chunk 164 optimal weight: 0.0370 chunk 108 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 259 optimal weight: 0.0470 chunk 232 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 253 optimal weight: 0.0870 chunk 260 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.216050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.163656 restraints weight = 29490.757| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 4.40 r_work: 0.3500 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27345 Z= 0.122 Angle : 0.567 8.090 37205 Z= 0.304 Chirality : 0.044 0.360 4080 Planarity : 0.012 0.474 4795 Dihedral : 6.482 159.468 3742 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.90 % Favored : 92.95 % Rotamer: Outliers : 3.46 % Allowed : 20.04 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.10 (0.14), residues: 3335 helix: -0.32 (0.41), residues: 160 sheet: -0.03 (0.16), residues: 1070 loop : -1.18 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 34 TYR 0.015 0.001 TYR S 37 PHE 0.017 0.001 PHE E 73 TRP 0.010 0.001 TRP K 148 HIS 0.010 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00259 (27310) covalent geometry : angle 0.56701 (37195) SS BOND : bond 0.00193 ( 5) SS BOND : angle 0.63101 ( 10) hydrogen bonds : bond 0.03295 ( 710) hydrogen bonds : angle 6.21656 ( 1665) Misc. bond : bond 0.01024 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 317 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 TYR cc_start: 0.8636 (m-10) cc_final: 0.7703 (m-10) REVERT: C 76 LYS cc_start: 0.7724 (mttm) cc_final: 0.7403 (mtpt) REVERT: E 54 MET cc_start: 0.8774 (tpp) cc_final: 0.8383 (mmm) REVERT: E 123 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.6355 (m170) REVERT: F 148 ILE cc_start: 0.8477 (mt) cc_final: 0.8267 (tt) REVERT: G 76 LYS cc_start: 0.7470 (mttm) cc_final: 0.7180 (mtpt) REVERT: G 145 HIS cc_start: 0.7259 (p-80) cc_final: 0.6690 (p90) REVERT: G 198 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6811 (t70) REVERT: I 54 MET cc_start: 0.8689 (tpp) cc_final: 0.8389 (mmm) REVERT: I 123 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.6487 (m170) REVERT: M 123 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.6320 (m170) REVERT: M 124 ARG cc_start: 0.5183 (OUTLIER) cc_final: 0.4397 (ptp90) REVERT: N 146 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: O 23 ASP cc_start: 0.7009 (p0) cc_final: 0.6299 (m-30) REVERT: O 76 LYS cc_start: 0.7623 (mttm) cc_final: 0.7320 (mtpt) REVERT: Q 54 MET cc_start: 0.8682 (tpp) cc_final: 0.8416 (mmm) REVERT: Q 123 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.6537 (m170) REVERT: S 43 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8550 (t0) outliers start: 98 outliers final: 74 residues processed: 376 average time/residue: 0.1801 time to fit residues: 103.5698 Evaluate side-chains 379 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 297 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 146 GLN Chi-restraints excluded: chain N residue 170 GLN Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 123 HIS Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 263 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 0.0980 chunk 23 optimal weight: 0.0970 chunk 120 optimal weight: 20.0000 chunk 295 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 31 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 HIS ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 174 HIS O 31 ASN ** Q 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 174 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.205222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155389 restraints weight = 29781.414| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 4.18 r_work: 0.3310 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 27345 Z= 0.293 Angle : 0.771 10.139 37205 Z= 0.403 Chirality : 0.051 0.360 4080 Planarity : 0.012 0.448 4795 Dihedral : 7.779 155.204 3734 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.22 % Favored : 91.45 % Rotamer: Outliers : 4.69 % Allowed : 19.68 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.49 (0.14), residues: 3335 helix: -1.45 (0.39), residues: 190 sheet: -0.13 (0.16), residues: 1035 loop : -1.45 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 200 TYR 0.024 0.003 TYR S 11 PHE 0.021 0.003 PHE K 77 TRP 0.026 0.002 TRP C 148 HIS 0.012 0.002 HIS O 145 Details of bonding type rmsd covalent geometry : bond 0.00720 (27310) covalent geometry : angle 0.77066 (37195) SS BOND : bond 0.00043 ( 5) SS BOND : angle 0.93540 ( 10) hydrogen bonds : bond 0.04894 ( 710) hydrogen bonds : angle 6.24394 ( 1665) Misc. bond : bond 0.01057 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 338 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 HIS cc_start: 0.8239 (OUTLIER) cc_final: 0.6469 (m170) REVERT: B 101 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7865 (mtm) REVERT: B 171 TYR cc_start: 0.8865 (m-10) cc_final: 0.7938 (m-10) REVERT: C 76 LYS cc_start: 0.8076 (mttm) cc_final: 0.7806 (mtpt) REVERT: C 107 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7942 (mp) REVERT: C 122 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6272 (ptt) REVERT: G 144 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7772 (mt) REVERT: G 145 HIS cc_start: 0.7672 (p-80) cc_final: 0.7396 (p90) REVERT: G 198 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6873 (t70) REVERT: I 54 MET cc_start: 0.8762 (tpp) cc_final: 0.8537 (mmm) REVERT: K 78 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7021 (m-30) REVERT: M 124 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.6034 (ptp90) REVERT: N 125 MET cc_start: 0.8630 (mmt) cc_final: 0.8147 (mmm) REVERT: O 37 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: O 76 LYS cc_start: 0.7993 (mttm) cc_final: 0.7408 (mtpt) REVERT: Q 54 MET cc_start: 0.8784 (tpp) cc_final: 0.8584 (mmm) REVERT: Q 123 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.5888 (m170) REVERT: Q 161 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8273 (p) REVERT: R 154 MET cc_start: 0.6553 (mmm) cc_final: 0.6290 (mmp) REVERT: S 110 MET cc_start: 0.7700 (tmm) cc_final: 0.7483 (tmm) outliers start: 133 outliers final: 91 residues processed: 434 average time/residue: 0.1656 time to fit residues: 111.8800 Evaluate side-chains 416 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 314 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 123 HIS Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 166 ASN Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 123 VAL Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 255 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 chunk 148 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 324 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 29 HIS ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.208234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157937 restraints weight = 29538.967| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 4.16 r_work: 0.3341 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 27345 Z= 0.172 Angle : 0.640 16.761 37205 Z= 0.339 Chirality : 0.046 0.372 4080 Planarity : 0.010 0.297 4795 Dihedral : 7.434 157.817 3734 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.14 % Favored : 92.68 % Rotamer: Outliers : 4.48 % Allowed : 20.04 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.49 (0.14), residues: 3335 helix: -1.43 (0.38), residues: 190 sheet: -0.14 (0.16), residues: 1045 loop : -1.45 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.001 ARG O 34 TYR 0.014 0.002 TYR O 30 PHE 0.016 0.002 PHE H 47 TRP 0.018 0.001 TRP C 148 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00403 (27310) covalent geometry : angle 0.64051 (37195) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.55769 ( 10) hydrogen bonds : bond 0.03864 ( 710) hydrogen bonds : angle 6.06649 ( 1665) Misc. bond : bond 0.00969 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 319 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: A 123 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.6924 (m90) REVERT: B 171 TYR cc_start: 0.8833 (m-10) cc_final: 0.8025 (m-10) REVERT: C 76 LYS cc_start: 0.8069 (mttm) cc_final: 0.7797 (mtpt) REVERT: C 107 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7866 (mp) REVERT: E 123 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.5267 (m170) REVERT: F 148 ILE cc_start: 0.8569 (mt) cc_final: 0.8318 (tt) REVERT: G 144 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7856 (mt) REVERT: G 145 HIS cc_start: 0.7771 (p-80) cc_final: 0.7545 (p90) REVERT: G 198 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.6994 (t70) REVERT: I 54 MET cc_start: 0.8771 (tpp) cc_final: 0.8478 (mmm) REVERT: I 123 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.6840 (m170) REVERT: M 123 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.6594 (m170) REVERT: M 124 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.5575 (ptp90) REVERT: N 125 MET cc_start: 0.8629 (mmt) cc_final: 0.8246 (mmm) REVERT: N 146 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: O 37 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: O 76 LYS cc_start: 0.7950 (mttm) cc_final: 0.7336 (mttt) REVERT: Q 128 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7502 (p) REVERT: R 154 MET cc_start: 0.6579 (mmm) cc_final: 0.6335 (mmp) REVERT: S 35 THR cc_start: 0.8915 (t) cc_final: 0.8703 (p) REVERT: S 110 MET cc_start: 0.7680 (tmm) cc_final: 0.7439 (tmm) outliers start: 127 outliers final: 87 residues processed: 403 average time/residue: 0.1659 time to fit residues: 103.4819 Evaluate side-chains 404 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 305 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 146 GLN Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 193 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 262 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 177 optimal weight: 0.1980 chunk 217 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 HIS ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** O 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 HIS ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.206998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157632 restraints weight = 29458.900| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 4.09 r_work: 0.3338 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 27345 Z= 0.193 Angle : 0.666 23.193 37205 Z= 0.350 Chirality : 0.047 0.461 4080 Planarity : 0.011 0.389 4795 Dihedral : 7.076 163.111 3734 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.98 % Favored : 91.87 % Rotamer: Outliers : 4.48 % Allowed : 20.21 % Favored : 75.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.55 (0.14), residues: 3335 helix: -1.91 (0.34), residues: 220 sheet: -0.07 (0.16), residues: 1025 loop : -1.48 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG G 34 TYR 0.021 0.002 TYR T 60 PHE 0.014 0.002 PHE D 47 TRP 0.017 0.001 TRP G 148 HIS 0.005 0.001 HIS M 28 Details of bonding type rmsd covalent geometry : bond 0.00467 (27310) covalent geometry : angle 0.66607 (37195) SS BOND : bond 0.00209 ( 5) SS BOND : angle 0.56634 ( 10) hydrogen bonds : bond 0.03957 ( 710) hydrogen bonds : angle 5.98810 ( 1665) Misc. bond : bond 0.00916 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 316 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: A 123 HIS cc_start: 0.8251 (OUTLIER) cc_final: 0.6720 (m170) REVERT: B 171 TYR cc_start: 0.8866 (m-10) cc_final: 0.8046 (m-10) REVERT: C 76 LYS cc_start: 0.8019 (mttm) cc_final: 0.7792 (mtpt) REVERT: C 107 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7929 (mp) REVERT: C 120 ARG cc_start: 0.6421 (mmt90) cc_final: 0.5864 (tpp-160) REVERT: E 123 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.5487 (m170) REVERT: F 148 ILE cc_start: 0.8577 (mt) cc_final: 0.8315 (tt) REVERT: G 110 MET cc_start: 0.6556 (ttt) cc_final: 0.6346 (tmm) REVERT: G 198 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7019 (t70) REVERT: I 54 MET cc_start: 0.8756 (tpp) cc_final: 0.8481 (mmm) REVERT: J 166 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7862 (m-40) REVERT: L 72 ARG cc_start: 0.8011 (ptp-110) cc_final: 0.7753 (ptp-110) REVERT: M 123 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.6582 (m170) REVERT: N 125 MET cc_start: 0.8646 (mmt) cc_final: 0.8265 (mmm) REVERT: O 37 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: O 76 LYS cc_start: 0.7967 (mttm) cc_final: 0.7498 (mttm) REVERT: R 154 MET cc_start: 0.6602 (mmm) cc_final: 0.6382 (mmp) REVERT: S 43 ASN cc_start: 0.9284 (OUTLIER) cc_final: 0.9048 (t0) REVERT: S 110 MET cc_start: 0.7667 (tmm) cc_final: 0.7424 (tmm) outliers start: 127 outliers final: 98 residues processed: 405 average time/residue: 0.1656 time to fit residues: 104.5376 Evaluate side-chains 410 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 303 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 122 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 123 VAL Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 166 ASN Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 123 VAL Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 123 VAL Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 148 optimal weight: 0.9990 chunk 230 optimal weight: 0.7980 chunk 143 optimal weight: 0.0030 chunk 170 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.210231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.161179 restraints weight = 29553.122| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 3.99 r_work: 0.3373 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27345 Z= 0.118 Angle : 0.624 27.036 37205 Z= 0.327 Chirality : 0.045 0.387 4080 Planarity : 0.013 0.444 4795 Dihedral : 5.980 130.118 3734 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.60 % Favored : 93.25 % Rotamer: Outliers : 3.77 % Allowed : 20.88 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.28 (0.14), residues: 3335 helix: -1.23 (0.37), residues: 190 sheet: 0.00 (0.16), residues: 1055 loop : -1.31 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG K 34 TYR 0.015 0.001 TYR K 37 PHE 0.018 0.001 PHE L 47 TRP 0.014 0.001 TRP S 148 HIS 0.004 0.001 HIS O 145 Details of bonding type rmsd covalent geometry : bond 0.00263 (27310) covalent geometry : angle 0.62379 (37195) SS BOND : bond 0.00298 ( 5) SS BOND : angle 0.40700 ( 10) hydrogen bonds : bond 0.03294 ( 710) hydrogen bonds : angle 5.78628 ( 1665) Misc. bond : bond 0.00758 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 319 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: B 171 TYR cc_start: 0.8828 (m-10) cc_final: 0.8060 (m-10) REVERT: C 76 LYS cc_start: 0.7945 (mttm) cc_final: 0.7740 (mtpt) REVERT: C 107 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7836 (mp) REVERT: E 54 MET cc_start: 0.8655 (tpp) cc_final: 0.8401 (mmm) REVERT: F 148 ILE cc_start: 0.8565 (mt) cc_final: 0.8285 (tt) REVERT: G 43 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8712 (t0) REVERT: G 110 MET cc_start: 0.6662 (ttt) cc_final: 0.6408 (tmm) REVERT: G 198 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6920 (t70) REVERT: H 83 MET cc_start: 0.4956 (tpt) cc_final: 0.4743 (tpt) REVERT: I 54 MET cc_start: 0.8721 (tpp) cc_final: 0.8428 (mmm) REVERT: L 72 ARG cc_start: 0.7928 (ptp-110) cc_final: 0.7655 (ptp-110) REVERT: L 83 MET cc_start: 0.5061 (tpt) cc_final: 0.4773 (tpt) REVERT: M 123 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.6599 (m170) REVERT: M 124 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.5019 (ptp90) REVERT: N 125 MET cc_start: 0.8629 (mmt) cc_final: 0.8340 (mmm) REVERT: N 146 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: O 76 LYS cc_start: 0.8000 (mttm) cc_final: 0.7494 (mttm) REVERT: P 83 MET cc_start: 0.4699 (tpt) cc_final: 0.4286 (tpt) REVERT: S 43 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.9055 (t0) REVERT: S 110 MET cc_start: 0.7676 (tmm) cc_final: 0.7452 (tmm) outliers start: 107 outliers final: 81 residues processed: 388 average time/residue: 0.1699 time to fit residues: 102.0304 Evaluate side-chains 397 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 308 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 174 GLU Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 146 GLN Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 31 TYR Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain S residue 187 ILE Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 176 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.207443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158025 restraints weight = 29136.622| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 4.05 r_work: 0.3319 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27345 Z= 0.194 Angle : 0.671 19.290 37205 Z= 0.350 Chirality : 0.048 0.522 4080 Planarity : 0.012 0.438 4795 Dihedral : 6.003 117.029 3734 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.86 % Favored : 91.99 % Rotamer: Outliers : 3.81 % Allowed : 21.02 % Favored : 75.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.47 (0.14), residues: 3335 helix: -1.84 (0.34), residues: 220 sheet: -0.05 (0.16), residues: 1045 loop : -1.42 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG S 34 TYR 0.016 0.002 TYR C 11 PHE 0.016 0.002 PHE S 77 TRP 0.017 0.001 TRP C 148 HIS 0.006 0.001 HIS I 123 Details of bonding type rmsd covalent geometry : bond 0.00474 (27310) covalent geometry : angle 0.67058 (37195) SS BOND : bond 0.00202 ( 5) SS BOND : angle 0.53101 ( 10) hydrogen bonds : bond 0.03875 ( 710) hydrogen bonds : angle 5.79995 ( 1665) Misc. bond : bond 0.00802 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 311 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: B 171 TYR cc_start: 0.8861 (m-10) cc_final: 0.8042 (m-10) REVERT: C 107 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7927 (mp) REVERT: F 148 ILE cc_start: 0.8589 (mt) cc_final: 0.8302 (tt) REVERT: G 110 MET cc_start: 0.6699 (ttt) cc_final: 0.6382 (tmm) REVERT: G 198 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6905 (t70) REVERT: I 54 MET cc_start: 0.8770 (tpp) cc_final: 0.8503 (mmm) REVERT: M 123 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.7111 (m90) REVERT: M 124 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.5763 (ptp90) REVERT: N 125 MET cc_start: 0.8679 (mmt) cc_final: 0.8373 (mmm) REVERT: N 146 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: O 76 LYS cc_start: 0.7895 (mttm) cc_final: 0.7530 (mttm) REVERT: P 83 MET cc_start: 0.4780 (tpt) cc_final: 0.4407 (tpt) REVERT: S 43 ASN cc_start: 0.9308 (OUTLIER) cc_final: 0.9060 (t0) REVERT: S 76 LYS cc_start: 0.7992 (mtpp) cc_final: 0.7715 (mmtt) outliers start: 108 outliers final: 94 residues processed: 384 average time/residue: 0.1973 time to fit residues: 117.3230 Evaluate side-chains 404 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 303 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 146 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 247 optimal weight: 1.9990 chunk 327 optimal weight: 20.0000 chunk 278 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 268 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 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 = 0.4364 r_free = 0.4364 target = 0.210010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.164260 restraints weight = 28852.405| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 3.61 r_work: 0.3357 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27345 Z= 0.130 Angle : 0.622 24.846 37205 Z= 0.328 Chirality : 0.045 0.427 4080 Planarity : 0.012 0.387 4795 Dihedral : 6.260 131.574 3734 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 3.60 % Allowed : 21.09 % Favored : 75.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.24 (0.14), residues: 3335 helix: -1.20 (0.37), residues: 190 sheet: 0.06 (0.16), residues: 1030 loop : -1.29 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG S 34 TYR 0.015 0.001 TYR K 37 PHE 0.019 0.001 PHE T 47 TRP 0.016 0.001 TRP H 112 HIS 0.004 0.001 HIS O 145 Details of bonding type rmsd covalent geometry : bond 0.00297 (27310) covalent geometry : angle 0.62249 (37195) SS BOND : bond 0.00287 ( 5) SS BOND : angle 0.40485 ( 10) hydrogen bonds : bond 0.03300 ( 710) hydrogen bonds : angle 5.64204 ( 1665) Misc. bond : bond 0.00822 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6670 Ramachandran restraints generated. 3335 Oldfield, 0 Emsley, 3335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 310 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: B 171 TYR cc_start: 0.8870 (m-10) cc_final: 0.8096 (m-10) REVERT: C 107 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7819 (mp) REVERT: E 54 MET cc_start: 0.8666 (tpp) cc_final: 0.8388 (mmm) REVERT: F 148 ILE cc_start: 0.8594 (mt) cc_final: 0.8309 (tt) REVERT: G 110 MET cc_start: 0.6711 (ttt) cc_final: 0.6418 (tmm) REVERT: G 198 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6909 (t70) REVERT: I 54 MET cc_start: 0.8739 (tpp) cc_final: 0.8437 (mmm) REVERT: L 72 ARG cc_start: 0.7956 (ptp-110) cc_final: 0.7706 (ptp-110) REVERT: M 123 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.6305 (m170) REVERT: M 124 ARG cc_start: 0.5466 (OUTLIER) cc_final: 0.4660 (ptp90) REVERT: N 125 MET cc_start: 0.8653 (mmt) cc_final: 0.8369 (mmm) REVERT: N 146 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: O 76 LYS cc_start: 0.7833 (mttm) cc_final: 0.7391 (mttt) REVERT: P 83 MET cc_start: 0.4514 (tpt) cc_final: 0.4271 (tpt) REVERT: S 43 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.9049 (t0) REVERT: S 76 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7773 (mmtt) outliers start: 102 outliers final: 91 residues processed: 378 average time/residue: 0.1782 time to fit residues: 104.2539 Evaluate side-chains 405 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 307 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 200 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 37 TYR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 143 CYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 174 GLU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 143 CYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 143 CYS Chi-restraints excluded: chain K residue 152 LEU Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 37 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 123 HIS Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 146 GLN Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 37 TYR Chi-restraints excluded: chain O residue 78 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 3 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 37 TYR Chi-restraints excluded: chain S residue 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain S residue 143 CYS Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain T residue 31 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 221 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 111 optimal weight: 0.0770 chunk 6 optimal weight: 0.0970 chunk 329 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 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 = 0.4364 r_free = 0.4364 target = 0.210007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.164030 restraints weight = 28866.518| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.60 r_work: 0.3354 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27345 Z= 0.135 Angle : 0.626 25.236 37205 Z= 0.327 Chirality : 0.045 0.440 4080 Planarity : 0.012 0.458 4795 Dihedral : 6.400 142.307 3733 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.99 % Favored : 92.86 % Rotamer: Outliers : 3.74 % Allowed : 21.16 % Favored : 75.10 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.22 (0.14), residues: 3335 helix: -1.11 (0.38), residues: 190 sheet: 0.04 (0.16), residues: 1055 loop : -1.28 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG C 34 TYR 0.020 0.001 TYR K 37 PHE 0.017 0.001 PHE L 47 TRP 0.014 0.001 TRP H 112 HIS 0.004 0.001 HIS O 145 Details of bonding type rmsd covalent geometry : bond 0.00311 (27310) covalent geometry : angle 0.62609 (37195) SS BOND : bond 0.00285 ( 5) SS BOND : angle 0.39779 ( 10) hydrogen bonds : bond 0.03308 ( 710) hydrogen bonds : angle 5.54874 ( 1665) Misc. bond : bond 0.00785 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6274.24 seconds wall clock time: 108 minutes 27.79 seconds (6507.79 seconds total)