Starting phenix.real_space_refine on Sun Jun 22 20:08:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8heg_34690/06_2025/8heg_34690.cif Found real_map, /net/cci-nas-00/data/ceres_data/8heg_34690/06_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_34690/06_2025/8heg_34690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8heg_34690/06_2025/8heg_34690.map" model { file = "/net/cci-nas-00/data/ceres_data/8heg_34690/06_2025/8heg_34690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8heg_34690/06_2025/8heg_34690.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: F, J, N, R, G, K, O, S, E, I, M, Q, H, L, P, T Time building chain proxies: 9.05, per 1000 atoms: 0.34 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: 6.57 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 3.66 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: 11.10 Time building geometry restraints manager: 7.81 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: 0.24 Found NCS groups: 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 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' } 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: 1.060 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: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 53.850 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.380 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: 0.020 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.650 ------------------------------------------------------------------------------- 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 : 16.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.001 TRP K 148 HIS 0.002 0.001 HIS M 49 PHE 0.014 0.002 PHE H 47 TYR 0.019 0.002 TYR L 60 ARG 0.006 0.001 ARG L 100 Details of bonding type rmsd hydrogen bonds : bond 0.26904 ( 710) hydrogen bonds : angle 9.08581 ( 1665) SS BOND : bond 0.00037 ( 5) SS BOND : angle 0.22607 ( 10) covalent geometry : bond 0.00409 (27310) covalent geometry : angle 0.70251 (37195) 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 : 2.858 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: 0.4219 time to fit residues: 239.9538 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 : 2.737 ------------------------------------------------------------------------------- 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 278 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 138 optimal weight: 0.0470 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 157 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS 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** F 209 HIS ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 HIS ** K 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 HIS ** O 31 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** R 209 HIS ** S 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.211210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156788 restraints weight = 29486.858| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 4.19 r_work: 0.3417 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27345 Z= 0.165 Angle : 0.667 8.116 37205 Z= 0.360 Chirality : 0.047 0.516 4080 Planarity : 0.008 0.164 4795 Dihedral : 5.740 48.105 3759 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.24 % Favored : 93.46 % Rotamer: Outliers : 3.56 % Allowed : 19.61 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3335 helix: -0.14 (0.42), residues: 160 sheet: -0.21 (0.16), residues: 1040 loop : -1.24 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 148 HIS 0.026 0.002 HIS Q 29 PHE 0.014 0.002 PHE E 73 TYR 0.023 0.002 TYR G 30 ARG 0.031 0.001 ARG I 114 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 710) hydrogen bonds : angle 7.09760 ( 1665) SS BOND : bond 0.00272 ( 5) SS BOND : angle 0.68291 ( 10) covalent geometry : bond 0.00376 (27310) covalent geometry : angle 0.66749 (37195) Misc. bond : bond 0.00985 ( 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 428 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 327 time to evaluate : 2.688 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 101 MET cc_start: 0.7672 (mtm) cc_final: 0.7462 (mtp) REVERT: C 120 ARG cc_start: 0.5988 (mmt90) cc_final: 0.5704 (mmm-85) REVERT: C 145 HIS cc_start: 0.6987 (p90) cc_final: 0.6634 (p90) REVERT: D 60 TYR cc_start: 0.7535 (m-80) cc_final: 0.6986 (m-80) REVERT: E 54 MET cc_start: 0.8787 (tpp) cc_final: 0.8521 (mmm) REVERT: E 65 LEU cc_start: 0.8989 (mt) cc_final: 0.8624 (mt) REVERT: E 125 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8089 (m) REVERT: G 145 HIS cc_start: 0.6747 (p-80) cc_final: 0.6329 (p90) REVERT: I 54 MET cc_start: 0.8657 (tpp) cc_final: 0.8328 (mmm) REVERT: I 125 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8014 (m) REVERT: J 59 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6827 (mt-10) REVERT: J 62 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.5798 (p90) REVERT: J 182 MET cc_start: 0.9135 (ttp) cc_final: 0.8908 (ttp) REVERT: M 125 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8135 (m) REVERT: N 101 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7733 (mtp) REVERT: O 86 MET cc_start: 0.8830 (mmm) cc_final: 0.8350 (mmm) REVERT: Q 54 MET cc_start: 0.8673 (tpp) cc_final: 0.8374 (mmm) REVERT: Q 125 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8144 (m) REVERT: R 59 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6980 (mt-10) REVERT: R 101 MET cc_start: 0.7706 (mtm) cc_final: 0.7092 (mtp) REVERT: R 196 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6098 (tt0) REVERT: S 34 ARG cc_start: 0.7660 (mmt180) cc_final: 0.7361 (mtm-85) REVERT: S 120 ARG cc_start: 0.6075 (mmm-85) cc_final: 0.5802 (mmt90) REVERT: S 122 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6158 (ptt) outliers start: 101 outliers final: 49 residues processed: 397 average time/residue: 0.4213 time to fit residues: 253.4858 Evaluate side-chains 354 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 125 VAL 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 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 152 LEU Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 37 ASP 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 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 152 LEU Chi-restraints excluded: chain H residue 31 TYR 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 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 152 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 101 MET 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 80 SER Chi-restraints excluded: chain P residue 58 THR 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 R residue 196 GLU 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 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 322 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 167 optimal weight: 0.1980 chunk 119 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 31 ASN ** 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** G 31 ASN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN O 145 HIS ** 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** S 31 ASN ** 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 = 0.4411 r_free = 0.4411 target = 0.215360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169317 restraints weight = 29426.746| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.48 r_work: 0.3469 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 27345 Z= 0.150 Angle : 0.605 9.169 37205 Z= 0.324 Chirality : 0.044 0.308 4080 Planarity : 0.013 0.457 4795 Dihedral : 5.883 118.577 3741 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.96 % Favored : 92.89 % Rotamer: Outliers : 3.42 % Allowed : 19.54 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3335 helix: -0.21 (0.42), residues: 160 sheet: -0.08 (0.16), residues: 1070 loop : -1.19 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 148 HIS 0.013 0.001 HIS E 29 PHE 0.025 0.001 PHE E 73 TYR 0.022 0.001 TYR K 30 ARG 0.031 0.001 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 710) hydrogen bonds : angle 6.60832 ( 1665) SS BOND : bond 0.00144 ( 5) SS BOND : angle 0.73987 ( 10) covalent geometry : bond 0.00345 (27310) covalent geometry : angle 0.60530 (37195) Misc. bond : bond 0.01044 ( 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 413 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 316 time to evaluate : 2.914 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: B 66 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7372 (mp) REVERT: B 108 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7590 (mm-30) REVERT: B 171 TYR cc_start: 0.8612 (m-10) cc_final: 0.7736 (m-10) REVERT: C 120 ARG cc_start: 0.6229 (mmt90) cc_final: 0.6008 (mmm-85) REVERT: C 145 HIS cc_start: 0.7163 (p90) cc_final: 0.6738 (p90) REVERT: D 60 TYR cc_start: 0.7731 (m-80) cc_final: 0.7043 (m-80) REVERT: F 148 ILE cc_start: 0.8543 (mt) cc_final: 0.8336 (tt) REVERT: G 145 HIS cc_start: 0.7078 (p-80) cc_final: 0.6603 (p90) REVERT: G 198 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6903 (t70) REVERT: I 54 MET cc_start: 0.8716 (tpp) cc_final: 0.8385 (mmm) REVERT: J 59 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6837 (mt-10) REVERT: J 182 MET cc_start: 0.9173 (ttp) cc_final: 0.8971 (ttp) REVERT: N 101 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7918 (mtp) REVERT: O 86 MET cc_start: 0.8858 (mmm) cc_final: 0.8420 (mmm) REVERT: Q 54 MET cc_start: 0.8726 (tpp) cc_final: 0.8431 (mmm) REVERT: R 101 MET cc_start: 0.7824 (mtm) cc_final: 0.7187 (mtp) REVERT: S 34 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7471 (mtm-85) outliers start: 97 outliers final: 67 residues processed: 380 average time/residue: 0.4104 time to fit residues: 240.4339 Evaluate side-chains 368 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 298 time to evaluate : 2.819 ------------------------------------------------------------------------------- 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 62 VAL Chi-restraints excluded: chain A residue 125 VAL 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 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 62 VAL Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 56 THR 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 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 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 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 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 50 VAL Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 101 MET Chi-restraints excluded: chain N residue 108 GLU 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 114 SER Chi-restraints excluded: chain O residue 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 126 VAL 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 137 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 319 optimal weight: 0.0670 chunk 264 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 275 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 1.3320 ------------------------------------------------------------------------------- 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 174 HIS 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** F 174 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 28 HIS ** 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 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** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.213522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.167419 restraints weight = 29782.389| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.63 r_work: 0.3442 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27345 Z= 0.147 Angle : 0.608 14.089 37205 Z= 0.320 Chirality : 0.045 0.342 4080 Planarity : 0.010 0.318 4795 Dihedral : 6.579 148.838 3736 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.90 % Favored : 92.95 % Rotamer: Outliers : 3.46 % Allowed : 19.86 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3335 helix: -0.24 (0.42), residues: 160 sheet: -0.08 (0.16), residues: 1070 loop : -1.21 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 148 HIS 0.012 0.001 HIS E 29 PHE 0.020 0.002 PHE Q 73 TYR 0.022 0.001 TYR K 30 ARG 0.017 0.001 ARG G 34 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 710) hydrogen bonds : angle 6.22476 ( 1665) SS BOND : bond 0.00110 ( 5) SS BOND : angle 0.80022 ( 10) covalent geometry : bond 0.00337 (27310) covalent geometry : angle 0.60750 (37195) Misc. bond : bond 0.00861 ( 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 409 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 311 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: C 120 ARG cc_start: 0.6174 (mmt90) cc_final: 0.5937 (mmm-85) REVERT: E 54 MET cc_start: 0.8803 (tpp) cc_final: 0.8424 (mmm) REVERT: F 148 ILE cc_start: 0.8563 (mt) cc_final: 0.8354 (tt) REVERT: G 43 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8668 (t0) REVERT: G 145 HIS cc_start: 0.7311 (p-80) cc_final: 0.7015 (p-80) REVERT: G 198 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6696 (t70) REVERT: I 54 MET cc_start: 0.8711 (tpp) cc_final: 0.8431 (mmm) REVERT: I 123 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.6614 (m170) REVERT: M 123 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.6479 (m170) REVERT: M 124 ARG cc_start: 0.5565 (OUTLIER) cc_final: 0.4706 (ptp90) REVERT: Q 54 MET cc_start: 0.8749 (tpp) cc_final: 0.8496 (mmm) REVERT: R 101 MET cc_start: 0.7920 (mtm) cc_final: 0.7235 (mtp) REVERT: R 196 GLU cc_start: 0.6522 (tt0) cc_final: 0.5931 (tp30) REVERT: S 43 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8545 (t0) outliers start: 98 outliers final: 71 residues processed: 372 average time/residue: 0.4318 time to fit residues: 248.0351 Evaluate side-chains 375 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 297 time to evaluate : 3.072 ------------------------------------------------------------------------------- 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 161 SER 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 108 GLU 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 104 THR 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 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 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 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 123 HIS Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 56 THR 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 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 123 HIS Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain N residue 56 THR 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 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 161 SER Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain S residue 43 ASN 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 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 89 optimal weight: 0.0030 chunk 141 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 271 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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** ** 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** R 174 HIS ** 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 = 0.4396 r_free = 0.4396 target = 0.213784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168744 restraints weight = 29476.681| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 3.61 r_work: 0.3425 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27345 Z= 0.133 Angle : 0.582 10.975 37205 Z= 0.307 Chirality : 0.044 0.360 4080 Planarity : 0.012 0.475 4795 Dihedral : 6.751 152.779 3728 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.93 % Favored : 92.89 % Rotamer: Outliers : 3.39 % Allowed : 20.42 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3335 helix: -0.22 (0.42), residues: 160 sheet: 0.01 (0.16), residues: 1080 loop : -1.18 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 148 HIS 0.008 0.001 HIS E 29 PHE 0.015 0.001 PHE H 47 TYR 0.014 0.001 TYR K 30 ARG 0.028 0.001 ARG O 34 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 710) hydrogen bonds : angle 6.00006 ( 1665) SS BOND : bond 0.00163 ( 5) SS BOND : angle 0.66619 ( 10) covalent geometry : bond 0.00302 (27310) covalent geometry : angle 0.58149 (37195) Misc. bond : bond 0.00904 ( 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 413 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 317 time to evaluate : 2.762 Fit side-chains REVERT: A 123 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.6407 (m170) REVERT: B 108 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: B 171 TYR cc_start: 0.8643 (m-10) cc_final: 0.7765 (m-10) REVERT: C 23 ASP cc_start: 0.7134 (p0) cc_final: 0.6891 (p0) REVERT: D 83 MET cc_start: 0.5171 (tpt) cc_final: 0.4960 (tpt) REVERT: E 54 MET cc_start: 0.8804 (tpp) cc_final: 0.8445 (mmm) REVERT: F 148 ILE cc_start: 0.8532 (mt) cc_final: 0.8255 (pt) REVERT: F 196 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6329 (tt0) REVERT: G 43 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8687 (t0) REVERT: G 144 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7735 (mt) REVERT: G 145 HIS cc_start: 0.7402 (p-80) cc_final: 0.7113 (p-80) REVERT: G 198 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6800 (t70) REVERT: I 54 MET cc_start: 0.8693 (tpp) cc_final: 0.8419 (mmm) REVERT: I 123 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.6503 (m170) REVERT: J 108 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7881 (mm-30) REVERT: M 123 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.6474 (m170) REVERT: O 76 LYS cc_start: 0.7665 (mttm) cc_final: 0.7400 (mtpt) REVERT: Q 54 MET cc_start: 0.8758 (tpp) cc_final: 0.8495 (mmm) REVERT: Q 123 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.6724 (m170) REVERT: R 101 MET cc_start: 0.7857 (mtm) cc_final: 0.7210 (mtp) REVERT: S 43 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8545 (t0) REVERT: S 76 LYS cc_start: 0.7605 (mttm) cc_final: 0.7350 (mtpt) outliers start: 96 outliers final: 70 residues processed: 375 average time/residue: 0.4281 time to fit residues: 248.6368 Evaluate side-chains 378 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 298 time to evaluate : 5.175 ------------------------------------------------------------------------------- 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 123 HIS Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 108 GLU 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 114 SER Chi-restraints excluded: chain C residue 143 CYS 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 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 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 144 ILE 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 J residue 56 THR 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 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 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 37 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 N residue 56 THR Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain O residue 3 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 143 CYS Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 31 TYR 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 174 GLU Chi-restraints excluded: chain R residue 126 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 201 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 308 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** G 31 ASN 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** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 174 HIS 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** ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN N 174 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** S 36 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 = 0.4372 r_free = 0.4372 target = 0.210530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.165445 restraints weight = 29058.250| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.65 r_work: 0.3399 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 27345 Z= 0.183 Angle : 0.648 20.757 37205 Z= 0.337 Chirality : 0.046 0.325 4080 Planarity : 0.013 0.439 4795 Dihedral : 6.612 159.082 3728 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.14 % Favored : 92.68 % Rotamer: Outliers : 4.20 % Allowed : 19.86 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3335 helix: -0.28 (0.43), residues: 160 sheet: -0.00 (0.16), residues: 1080 loop : -1.23 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 148 HIS 0.007 0.001 HIS E 29 PHE 0.017 0.002 PHE H 47 TYR 0.015 0.002 TYR C 11 ARG 0.024 0.001 ARG K 34 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 710) hydrogen bonds : angle 5.95933 ( 1665) SS BOND : bond 0.00133 ( 5) SS BOND : angle 0.70829 ( 10) covalent geometry : bond 0.00440 (27310) covalent geometry : angle 0.64794 (37195) Misc. bond : bond 0.00898 ( 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 437 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 318 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.6701 (m170) REVERT: A 161 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8405 (p) REVERT: B 171 TYR cc_start: 0.8727 (m-10) cc_final: 0.7803 (m-10) REVERT: E 54 MET cc_start: 0.8761 (tpp) cc_final: 0.8456 (mmm) REVERT: E 123 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.6816 (m170) REVERT: F 148 ILE cc_start: 0.8546 (mt) cc_final: 0.8264 (pt) REVERT: G 35 THR cc_start: 0.8716 (t) cc_final: 0.8514 (p) REVERT: G 43 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8669 (t0) REVERT: G 144 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7825 (mt) REVERT: G 198 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6812 (t70) REVERT: I 54 MET cc_start: 0.8734 (tpp) cc_final: 0.8458 (mmm) REVERT: J 108 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7911 (mm-30) REVERT: K 35 THR cc_start: 0.8536 (t) cc_final: 0.8282 (p) REVERT: M 123 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.6466 (m170) REVERT: N 125 MET cc_start: 0.8429 (mmt) cc_final: 0.7930 (mmm) REVERT: O 76 LYS cc_start: 0.7778 (mttm) cc_final: 0.7271 (mtpt) REVERT: Q 54 MET cc_start: 0.8800 (tpp) cc_final: 0.8534 (mmm) REVERT: Q 123 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.6213 (m170) REVERT: R 101 MET cc_start: 0.8063 (mtm) cc_final: 0.7422 (mtp) REVERT: R 196 GLU cc_start: 0.6950 (tt0) cc_final: 0.6491 (tp30) REVERT: S 43 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8976 (t0) REVERT: S 76 LYS cc_start: 0.7721 (mttm) cc_final: 0.7469 (mtpt) REVERT: S 110 MET cc_start: 0.7527 (tmm) cc_final: 0.7321 (tmm) outliers start: 119 outliers final: 89 residues processed: 403 average time/residue: 0.5219 time to fit residues: 334.7092 Evaluate side-chains 407 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 309 time to evaluate : 2.919 ------------------------------------------------------------------------------- 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 62 VAL Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 161 SER 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 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 114 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 143 CYS 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 95 GLU Chi-restraints excluded: chain E residue 123 HIS 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 109 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 36 ASN 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 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 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 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 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 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 56 THR 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 21 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 O residue 171 THR 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 174 GLU Chi-restraints excluded: chain Q residue 200 ARG 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 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR 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 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 60 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 204 optimal weight: 0.0970 chunk 101 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 138 optimal weight: 0.0470 overall best weight: 0.7878 ------------------------------------------------------------------------------- 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** ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** 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 29 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** S 36 ASN ** 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 = 0.4395 r_free = 0.4395 target = 0.212987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163729 restraints weight = 29068.984| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.81 r_work: 0.3415 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27345 Z= 0.119 Angle : 0.572 10.214 37205 Z= 0.303 Chirality : 0.044 0.319 4080 Planarity : 0.010 0.327 4795 Dihedral : 6.597 161.830 3728 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 3.99 % Allowed : 20.07 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3335 helix: -0.26 (0.42), residues: 160 sheet: 0.09 (0.16), residues: 1080 loop : -1.17 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 148 HIS 0.006 0.001 HIS M 29 PHE 0.014 0.001 PHE D 47 TYR 0.013 0.001 TYR K 30 ARG 0.027 0.001 ARG K 34 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 710) hydrogen bonds : angle 5.77623 ( 1665) SS BOND : bond 0.00237 ( 5) SS BOND : angle 0.47874 ( 10) covalent geometry : bond 0.00268 (27310) covalent geometry : angle 0.57187 (37195) Misc. bond : bond 0.00844 ( 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 425 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 312 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.6103 (m170) REVERT: B 171 TYR cc_start: 0.8693 (m-10) cc_final: 0.7820 (m-10) REVERT: C 23 ASP cc_start: 0.7305 (p0) cc_final: 0.6813 (m-30) REVERT: C 120 ARG cc_start: 0.6181 (mmt90) cc_final: 0.5869 (mmm-85) REVERT: E 54 MET cc_start: 0.8727 (tpp) cc_final: 0.8411 (mmm) REVERT: F 148 ILE cc_start: 0.8535 (mt) cc_final: 0.8291 (pt) REVERT: G 43 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8703 (t0) REVERT: I 54 MET cc_start: 0.8646 (tpp) cc_final: 0.8355 (mmm) REVERT: I 123 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.6814 (m170) REVERT: K 120 ARG cc_start: 0.6158 (tpp80) cc_final: 0.5825 (tpp-160) REVERT: M 123 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.6480 (m170) REVERT: O 23 ASP cc_start: 0.7210 (p0) cc_final: 0.6579 (m-30) REVERT: O 76 LYS cc_start: 0.7635 (mttm) cc_final: 0.7087 (mtpt) REVERT: Q 54 MET cc_start: 0.8744 (tpp) cc_final: 0.8493 (mmm) REVERT: Q 123 HIS cc_start: 0.7950 (OUTLIER) cc_final: 0.5864 (m170) REVERT: R 101 MET cc_start: 0.7828 (mtm) cc_final: 0.7194 (mtp) REVERT: R 196 GLU cc_start: 0.6889 (tt0) cc_final: 0.6518 (tp30) REVERT: S 43 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8932 (t0) REVERT: S 76 LYS cc_start: 0.7712 (mttm) cc_final: 0.7445 (mtpt) REVERT: S 110 MET cc_start: 0.7525 (tmm) cc_final: 0.7299 (tmm) outliers start: 113 outliers final: 77 residues processed: 387 average time/residue: 0.4267 time to fit residues: 253.9064 Evaluate side-chains 385 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 302 time to evaluate : 3.148 ------------------------------------------------------------------------------- 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 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 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 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 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 125 VAL 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 G residue 3 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 H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 123 HIS 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 37 TYR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 104 THR 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 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 96 ASP 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 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 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 174 GLU Chi-restraints excluded: chain Q residue 200 ARG 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 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 145 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 302 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 250 optimal weight: 0.9990 chunk 186 optimal weight: 30.0000 chunk 81 optimal weight: 0.3980 chunk 278 optimal weight: 4.9990 chunk 303 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 HIS ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS ** M 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** 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 = 0.4376 r_free = 0.4376 target = 0.211868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.166805 restraints weight = 29635.637| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.81 r_work: 0.3417 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27345 Z= 0.138 Angle : 0.621 28.970 37205 Z= 0.322 Chirality : 0.044 0.274 4080 Planarity : 0.011 0.364 4795 Dihedral : 7.273 157.635 3728 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % Rotamer: Outliers : 3.53 % Allowed : 20.21 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.14), residues: 3335 helix: -0.24 (0.43), residues: 160 sheet: 0.08 (0.16), residues: 1075 loop : -1.18 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 148 HIS 0.007 0.001 HIS M 29 PHE 0.017 0.001 PHE A 73 TYR 0.014 0.001 TYR S 37 ARG 0.015 0.001 ARG E 200 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 710) hydrogen bonds : angle 5.70274 ( 1665) SS BOND : bond 0.00215 ( 5) SS BOND : angle 0.52684 ( 10) covalent geometry : bond 0.00319 (27310) covalent geometry : angle 0.62095 (37195) Misc. bond : bond 0.00820 ( 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 412 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 312 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 ASP cc_start: 0.7396 (p0) cc_final: 0.6866 (m-30) REVERT: E 37 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: E 54 MET cc_start: 0.8752 (tpp) cc_final: 0.8431 (mmm) REVERT: F 148 ILE cc_start: 0.8551 (mt) cc_final: 0.8311 (pt) REVERT: G 43 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8732 (t0) REVERT: G 59 ASP cc_start: 0.7909 (t0) cc_final: 0.7667 (t0) REVERT: I 54 MET cc_start: 0.8691 (tpp) cc_final: 0.8416 (mmm) REVERT: I 123 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.6664 (m170) REVERT: K 120 ARG cc_start: 0.6266 (tpp80) cc_final: 0.5916 (tpp-160) REVERT: M 123 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.6345 (m170) REVERT: O 23 ASP cc_start: 0.7272 (p0) cc_final: 0.6658 (m-30) REVERT: O 76 LYS cc_start: 0.7751 (mttm) cc_final: 0.7206 (mtpt) REVERT: Q 54 MET cc_start: 0.8743 (tpp) cc_final: 0.8475 (mmm) REVERT: Q 123 HIS cc_start: 0.8034 (OUTLIER) cc_final: 0.6135 (m170) REVERT: R 101 MET cc_start: 0.7866 (mtm) cc_final: 0.7231 (mtp) REVERT: R 196 GLU cc_start: 0.6996 (tt0) cc_final: 0.6631 (tp30) REVERT: S 43 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8961 (t0) REVERT: S 110 MET cc_start: 0.7547 (tmm) cc_final: 0.7338 (tmm) outliers start: 100 outliers final: 79 residues processed: 381 average time/residue: 0.3868 time to fit residues: 228.9687 Evaluate side-chains 390 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 305 time to evaluate : 2.608 ------------------------------------------------------------------------------- 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 161 SER 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 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 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 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 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 G residue 3 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 H residue 31 TYR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 80 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 122 MET 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 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 56 THR Chi-restraints excluded: chain N residue 96 ASP 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 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 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 174 GLU Chi-restraints excluded: chain Q residue 200 ARG 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 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 150 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 328 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.213443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167763 restraints weight = 29600.093| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 3.58 r_work: 0.3413 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27345 Z= 0.115 Angle : 0.598 26.170 37205 Z= 0.311 Chirality : 0.044 0.522 4080 Planarity : 0.011 0.427 4795 Dihedral : 6.796 159.555 3728 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.33 % Favored : 93.55 % Rotamer: Outliers : 3.10 % Allowed : 20.63 % Favored : 76.26 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3335 helix: -0.21 (0.43), residues: 160 sheet: 0.10 (0.16), residues: 1080 loop : -1.15 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 148 HIS 0.004 0.001 HIS O 145 PHE 0.015 0.001 PHE H 47 TYR 0.014 0.001 TYR T 60 ARG 0.039 0.001 ARG C 34 Details of bonding type rmsd hydrogen bonds : bond 0.03086 ( 710) hydrogen bonds : angle 5.58934 ( 1665) SS BOND : bond 0.00240 ( 5) SS BOND : angle 0.46083 ( 10) covalent geometry : bond 0.00258 (27310) covalent geometry : angle 0.59829 (37195) Misc. bond : bond 0.00795 ( 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 391 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 303 time to evaluate : 3.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 23 ASP cc_start: 0.7239 (p0) cc_final: 0.6772 (m-30) REVERT: E 37 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7645 (m-30) REVERT: E 54 MET cc_start: 0.8821 (tpp) cc_final: 0.8429 (mmm) REVERT: E 123 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.6517 (m170) REVERT: F 148 ILE cc_start: 0.8538 (mt) cc_final: 0.8322 (pt) REVERT: G 43 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8713 (t0) REVERT: G 59 ASP cc_start: 0.7906 (t0) cc_final: 0.7680 (t0) REVERT: I 54 MET cc_start: 0.8661 (tpp) cc_final: 0.8380 (mmm) REVERT: K 120 ARG cc_start: 0.6148 (tpp80) cc_final: 0.5834 (tpp-160) REVERT: N 125 MET cc_start: 0.8459 (mmt) cc_final: 0.7993 (mmm) REVERT: O 23 ASP cc_start: 0.7196 (p0) cc_final: 0.6612 (m-30) REVERT: O 76 LYS cc_start: 0.7740 (mttm) cc_final: 0.7185 (mttt) REVERT: P 83 MET cc_start: 0.4623 (tpt) cc_final: 0.4180 (tpt) REVERT: P 112 TRP cc_start: 0.7924 (m100) cc_final: 0.7647 (m100) REVERT: Q 54 MET cc_start: 0.8717 (tpp) cc_final: 0.8450 (mmm) REVERT: R 101 MET cc_start: 0.7798 (mtm) cc_final: 0.7158 (mtp) REVERT: R 196 GLU cc_start: 0.6952 (tt0) cc_final: 0.6617 (tp30) REVERT: S 43 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8933 (t0) REVERT: S 110 MET cc_start: 0.7596 (tmm) cc_final: 0.7393 (tmm) REVERT: T 83 MET cc_start: 0.4643 (tpt) cc_final: 0.4358 (tpt) outliers start: 88 outliers final: 76 residues processed: 359 average time/residue: 0.4016 time to fit residues: 225.3715 Evaluate side-chains 382 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 302 time to evaluate : 2.595 ------------------------------------------------------------------------------- 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 161 SER 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 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 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 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 G residue 3 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 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 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 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 37 ASP Chi-restraints excluded: chain M residue 40 VAL 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 109 VAL Chi-restraints excluded: chain N residue 126 VAL 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 31 TYR Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 174 GLU Chi-restraints excluded: chain Q residue 200 ARG 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 43 ASN Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 104 THR 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 265 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 297 optimal weight: 5.9990 chunk 300 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** ** I 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 36 ASN ** L 6 GLN ** 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 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 = 0.4357 r_free = 0.4357 target = 0.209824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159791 restraints weight = 29458.891| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 4.06 r_work: 0.3385 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27345 Z= 0.150 Angle : 0.622 24.529 37205 Z= 0.325 Chirality : 0.045 0.287 4080 Planarity : 0.011 0.454 4795 Dihedral : 6.838 160.583 3728 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.14 % Favored : 92.74 % Rotamer: Outliers : 3.10 % Allowed : 20.74 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3335 helix: -0.90 (0.39), residues: 190 sheet: 0.03 (0.16), residues: 1095 loop : -1.18 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 112 HIS 0.006 0.001 HIS O 145 PHE 0.016 0.002 PHE H 68 TYR 0.015 0.002 TYR K 30 ARG 0.018 0.001 ARG S 34 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 710) hydrogen bonds : angle 5.56513 ( 1665) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.45209 ( 10) covalent geometry : bond 0.00356 (27310) covalent geometry : angle 0.62173 (37195) Misc. bond : bond 0.00774 ( 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 402 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 314 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.7876 (mtm) cc_final: 0.7618 (mtp) REVERT: C 23 ASP cc_start: 0.7075 (p0) cc_final: 0.6859 (m-30) REVERT: E 37 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7625 (m-30) REVERT: E 54 MET cc_start: 0.8764 (tpp) cc_final: 0.8462 (mmm) REVERT: E 123 HIS cc_start: 0.8535 (OUTLIER) cc_final: 0.5850 (m170) REVERT: F 148 ILE cc_start: 0.8563 (mt) cc_final: 0.8322 (tt) REVERT: I 54 MET cc_start: 0.8699 (tpp) cc_final: 0.8439 (mmm) REVERT: K 120 ARG cc_start: 0.6260 (tpp80) cc_final: 0.5943 (tpp-160) REVERT: L 72 ARG cc_start: 0.8017 (ptp-110) cc_final: 0.7765 (ptp-110) REVERT: N 125 MET cc_start: 0.8531 (mmt) cc_final: 0.8058 (mmm) REVERT: O 76 LYS cc_start: 0.7944 (mttm) cc_final: 0.7441 (mttt) REVERT: P 112 TRP cc_start: 0.7879 (m100) cc_final: 0.7615 (m100) REVERT: Q 54 MET cc_start: 0.8759 (tpp) cc_final: 0.8507 (mmm) REVERT: R 62 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6158 (p90) REVERT: R 101 MET cc_start: 0.7962 (mtm) cc_final: 0.7351 (mtp) REVERT: R 196 GLU cc_start: 0.7133 (tt0) cc_final: 0.6444 (tp30) REVERT: S 110 MET cc_start: 0.7569 (tmm) cc_final: 0.7367 (tmm) REVERT: T 83 MET cc_start: 0.4715 (tpt) cc_final: 0.4486 (tpt) outliers start: 88 outliers final: 75 residues processed: 374 average time/residue: 0.4037 time to fit residues: 234.1175 Evaluate side-chains 385 residues out of total 2840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 307 time to evaluate : 2.959 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 143 CYS 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 80 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 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 114 SER 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 37 ASP Chi-restraints excluded: chain M residue 40 VAL 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 109 VAL Chi-restraints excluded: chain N residue 126 VAL 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 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 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 174 GLU Chi-restraints excluded: chain Q residue 200 ARG Chi-restraints excluded: chain R residue 62 PHE 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 78 ASP Chi-restraints excluded: chain S residue 104 THR 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 239 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 chunk 260 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 199 optimal weight: 0.0980 chunk 181 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** ** 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** ** P 6 GLN ** 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 = 0.4343 r_free = 0.4343 target = 0.208366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.159233 restraints weight = 29610.657| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 4.07 r_work: 0.3343 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 27345 Z= 0.189 Angle : 0.684 23.326 37205 Z= 0.356 Chirality : 0.047 0.303 4080 Planarity : 0.013 0.466 4795 Dihedral : 6.813 146.814 3728 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.11 % Favored : 92.68 % Rotamer: Outliers : 3.25 % Allowed : 20.85 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3335 helix: -1.02 (0.38), residues: 190 sheet: 0.04 (0.16), residues: 1065 loop : -1.26 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP T 112 HIS 0.006 0.001 HIS O 145 PHE 0.018 0.002 PHE L 47 TYR 0.016 0.002 TYR C 11 ARG 0.041 0.001 ARG G 34 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 710) hydrogen bonds : angle 5.59245 ( 1665) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.49632 ( 10) covalent geometry : bond 0.00455 (27310) covalent geometry : angle 0.68437 (37195) Misc. bond : bond 0.00922 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14224.15 seconds wall clock time: 248 minutes 23.43 seconds (14903.43 seconds total)