Starting phenix.real_space_refine on Fri May 23 08:13:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwa_63436/05_2025/9lwa_63436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwa_63436/05_2025/9lwa_63436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lwa_63436/05_2025/9lwa_63436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwa_63436/05_2025/9lwa_63436.map" model { file = "/net/cci-nas-00/data/ceres_data/9lwa_63436/05_2025/9lwa_63436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwa_63436/05_2025/9lwa_63436.cif" } resolution = 3.83 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= -0.000 sd= 0.003 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 72 5.16 5 C 15144 2.51 5 N 4170 2.21 5 O 4686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24072 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 943 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 10, 'TRANS': 117} Chain: "B" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1072 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 8, 'TRANS': 127} Chain: "C" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1997 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 17, 'TRANS': 239} Restraints were copied for chains: E, H, K, N, Q, F, I, L, O, R, D, G, J, M, P Time building chain proxies: 8.52, per 1000 atoms: 0.35 Number of scatterers: 24072 At special positions: 0 Unit cell: (124.852, 127.596, 131.712, 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 72 16.00 O 4686 8.00 N 4170 7.00 C 15144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 3.0 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5664 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 60 sheets defined 16.1% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'B' and resid 13 through 23 Processing helix chain 'B' and resid 69 through 91 Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.697A pdb=" N SER C 42 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 149 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'D' and resid 22 through 26 Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'E' and resid 13 through 23 Processing helix chain 'E' and resid 69 through 91 Processing helix chain 'F' and resid 9 through 14 Processing helix chain 'F' and resid 19 through 23 Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.697A pdb=" N SER F 42 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 149 Processing helix chain 'F' and resid 254 through 259 Processing helix chain 'G' and resid 22 through 26 Processing helix chain 'G' and resid 68 through 73 Processing helix chain 'G' and resid 95 through 101 Processing helix chain 'H' and resid 13 through 23 Processing helix chain 'H' and resid 69 through 91 Processing helix chain 'I' and resid 9 through 14 Processing helix chain 'I' and resid 19 through 23 Processing helix chain 'I' and resid 39 through 44 removed outlier: 3.697A pdb=" N SER I 42 " --> pdb=" O LEU I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 149 Processing helix chain 'I' and resid 254 through 259 Processing helix chain 'J' and resid 22 through 26 Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 95 through 101 Processing helix chain 'K' and resid 13 through 23 Processing helix chain 'K' and resid 69 through 91 Processing helix chain 'L' and resid 9 through 14 Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 39 through 44 removed outlier: 3.697A pdb=" N SER L 42 " --> pdb=" O LEU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 149 Processing helix chain 'L' and resid 254 through 259 Processing helix chain 'M' and resid 22 through 26 Processing helix chain 'M' and resid 68 through 73 Processing helix chain 'M' and resid 95 through 101 Processing helix chain 'N' and resid 13 through 23 Processing helix chain 'N' and resid 69 through 91 Processing helix chain 'O' and resid 9 through 14 Processing helix chain 'O' and resid 19 through 23 Processing helix chain 'O' and resid 39 through 44 removed outlier: 3.698A pdb=" N SER O 42 " --> pdb=" O LEU O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 149 Processing helix chain 'O' and resid 254 through 259 Processing helix chain 'P' and resid 22 through 26 Processing helix chain 'P' and resid 68 through 73 Processing helix chain 'P' and resid 95 through 101 Processing helix chain 'Q' and resid 13 through 23 Processing helix chain 'Q' and resid 69 through 91 Processing helix chain 'R' and resid 9 through 14 Processing helix chain 'R' and resid 19 through 23 Processing helix chain 'R' and resid 39 through 44 removed outlier: 3.697A pdb=" N SER R 42 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 149 Processing helix chain 'R' and resid 254 through 259 Processing sheet with id=1, first strand: chain 'A' and resid 8 through 18 removed outlier: 5.910A pdb=" N GLN A 8 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 28 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 60 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A 46 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A 58 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS A 112 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL A 122 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET A 110 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 124 " --> pdb=" O PRO A 108 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N CYS A 126 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP A 106 " --> pdb=" O CYS A 126 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ARG A 128 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG A 104 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 80 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 9 through 10 Processing sheet with id=3, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.767A pdb=" N VAL B 43 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 60 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N ILE B 123 " --> pdb=" O MET B 116 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N MET B 116 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG B 125 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER B 114 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR B 127 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS B 112 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 129 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 133 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 106 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=5, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=6, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU C 30 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG C 182 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 205 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR C 226 " --> pdb=" O ASN C 209 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU C 30 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG C 182 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 205 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C 253 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS C 249 " --> pdb=" O ALA C 202 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=9, first strand: chain 'C' and resid 106 through 112 removed outlier: 7.107A pdb=" N SER C 106 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN C 128 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP C 108 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU C 122 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 236 through 238 removed outlier: 4.099A pdb=" N ALA C 237 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS C 244 " --> pdb=" O ALA C 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'D' and resid 8 through 18 removed outlier: 5.910A pdb=" N GLN D 8 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 28 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL D 60 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER D 46 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR D 58 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS D 112 " --> pdb=" O HIS D 120 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL D 122 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET D 110 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE D 124 " --> pdb=" O PRO D 108 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N CYS D 126 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP D 106 " --> pdb=" O CYS D 126 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG D 128 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG D 104 " --> pdb=" O ARG D 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 80 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 9 through 10 Processing sheet with id=13, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.767A pdb=" N VAL E 43 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL E 60 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N ILE E 123 " --> pdb=" O MET E 116 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N MET E 116 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG E 125 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER E 114 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR E 127 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS E 112 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG E 129 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY E 133 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE E 106 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=15, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=16, first strand: chain 'F' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU F 30 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG F 182 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU F 205 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR F 226 " --> pdb=" O ASN F 209 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU F 30 " --> pdb=" O ILE F 189 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG F 182 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU F 205 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY F 253 " --> pdb=" O TYR F 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS F 249 " --> pdb=" O ALA F 202 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'F' and resid 72 through 75 Processing sheet with id=19, first strand: chain 'F' and resid 106 through 112 removed outlier: 7.107A pdb=" N SER F 106 " --> pdb=" O GLN F 128 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN F 128 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP F 108 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 122 " --> pdb=" O GLN F 112 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'F' and resid 236 through 238 removed outlier: 4.099A pdb=" N ALA F 237 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS F 244 " --> pdb=" O ALA F 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=20 Processing sheet with id=21, first strand: chain 'G' and resid 8 through 18 removed outlier: 5.909A pdb=" N GLN G 8 " --> pdb=" O GLY G 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA G 28 " --> pdb=" O THR G 18 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL G 60 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER G 46 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR G 58 " --> pdb=" O SER G 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS G 112 " --> pdb=" O HIS G 120 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL G 122 " --> pdb=" O MET G 110 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET G 110 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE G 124 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N CYS G 126 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP G 106 " --> pdb=" O CYS G 126 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG G 128 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG G 104 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU G 80 " --> pdb=" O PHE G 103 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'H' and resid 9 through 10 Processing sheet with id=23, first strand: chain 'H' and resid 28 through 29 removed outlier: 3.768A pdb=" N VAL H 43 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL H 60 " --> pdb=" O ILE H 46 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N ILE H 123 " --> pdb=" O MET H 116 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N MET H 116 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG H 125 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER H 114 " --> pdb=" O ARG H 125 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR H 127 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS H 112 " --> pdb=" O THR H 127 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG H 129 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY H 133 " --> pdb=" O PHE H 106 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE H 106 " --> pdb=" O GLY H 133 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=25, first strand: chain 'H' and resid 94 through 95 Processing sheet with id=26, first strand: chain 'I' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU I 30 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG I 182 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU I 205 " --> pdb=" O ARG I 182 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR I 226 " --> pdb=" O ASN I 209 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'I' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU I 30 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG I 182 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU I 205 " --> pdb=" O ARG I 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY I 253 " --> pdb=" O TYR I 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS I 249 " --> pdb=" O ALA I 202 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'I' and resid 72 through 75 Processing sheet with id=29, first strand: chain 'I' and resid 106 through 112 removed outlier: 7.106A pdb=" N SER I 106 " --> pdb=" O GLN I 128 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN I 128 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP I 108 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU I 122 " --> pdb=" O GLN I 112 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'I' and resid 236 through 238 removed outlier: 4.098A pdb=" N ALA I 237 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS I 244 " --> pdb=" O ALA I 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=30 Processing sheet with id=31, first strand: chain 'J' and resid 8 through 18 removed outlier: 5.910A pdb=" N GLN J 8 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA J 28 " --> pdb=" O THR J 18 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL J 60 " --> pdb=" O ALA J 44 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER J 46 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR J 58 " --> pdb=" O SER J 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS J 112 " --> pdb=" O HIS J 120 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL J 122 " --> pdb=" O MET J 110 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET J 110 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE J 124 " --> pdb=" O PRO J 108 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N CYS J 126 " --> pdb=" O ASP J 106 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP J 106 " --> pdb=" O CYS J 126 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG J 128 " --> pdb=" O ARG J 104 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG J 104 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU J 80 " --> pdb=" O PHE J 103 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'K' and resid 9 through 10 Processing sheet with id=33, first strand: chain 'K' and resid 28 through 29 removed outlier: 3.768A pdb=" N VAL K 43 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL K 60 " --> pdb=" O ILE K 46 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N ILE K 123 " --> pdb=" O MET K 116 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N MET K 116 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG K 125 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER K 114 " --> pdb=" O ARG K 125 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR K 127 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS K 112 " --> pdb=" O THR K 127 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG K 129 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY K 133 " --> pdb=" O PHE K 106 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE K 106 " --> pdb=" O GLY K 133 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'K' and resid 50 through 51 Processing sheet with id=35, first strand: chain 'K' and resid 94 through 95 Processing sheet with id=36, first strand: chain 'L' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU L 30 " --> pdb=" O ILE L 189 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG L 182 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU L 205 " --> pdb=" O ARG L 182 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR L 226 " --> pdb=" O ASN L 209 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'L' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU L 30 " --> pdb=" O ILE L 189 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG L 182 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU L 205 " --> pdb=" O ARG L 182 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY L 253 " --> pdb=" O TYR L 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS L 249 " --> pdb=" O ALA L 202 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'L' and resid 72 through 75 Processing sheet with id=39, first strand: chain 'L' and resid 106 through 112 removed outlier: 7.107A pdb=" N SER L 106 " --> pdb=" O GLN L 128 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN L 128 " --> pdb=" O SER L 106 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP L 108 " --> pdb=" O THR L 126 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU L 122 " --> pdb=" O GLN L 112 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'L' and resid 236 through 238 removed outlier: 4.099A pdb=" N ALA L 237 " --> pdb=" O LYS L 244 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS L 244 " --> pdb=" O ALA L 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=40 Processing sheet with id=41, first strand: chain 'M' and resid 8 through 18 removed outlier: 5.909A pdb=" N GLN M 8 " --> pdb=" O GLY M 38 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA M 28 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL M 60 " --> pdb=" O ALA M 44 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER M 46 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR M 58 " --> pdb=" O SER M 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS M 112 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL M 122 " --> pdb=" O MET M 110 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N MET M 110 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE M 124 " --> pdb=" O PRO M 108 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N CYS M 126 " --> pdb=" O ASP M 106 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP M 106 " --> pdb=" O CYS M 126 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG M 128 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG M 104 " --> pdb=" O ARG M 128 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 80 " --> pdb=" O PHE M 103 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'N' and resid 9 through 10 Processing sheet with id=43, first strand: chain 'N' and resid 28 through 29 removed outlier: 3.767A pdb=" N VAL N 43 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL N 60 " --> pdb=" O ILE N 46 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N ILE N 123 " --> pdb=" O MET N 116 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N MET N 116 " --> pdb=" O ILE N 123 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG N 125 " --> pdb=" O SER N 114 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER N 114 " --> pdb=" O ARG N 125 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR N 127 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS N 112 " --> pdb=" O THR N 127 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG N 129 " --> pdb=" O LEU N 110 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY N 133 " --> pdb=" O PHE N 106 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE N 106 " --> pdb=" O GLY N 133 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'N' and resid 50 through 51 Processing sheet with id=45, first strand: chain 'N' and resid 94 through 95 Processing sheet with id=46, first strand: chain 'O' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU O 30 " --> pdb=" O ILE O 189 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG O 182 " --> pdb=" O LEU O 205 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU O 205 " --> pdb=" O ARG O 182 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR O 226 " --> pdb=" O ASN O 209 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'O' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU O 30 " --> pdb=" O ILE O 189 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG O 182 " --> pdb=" O LEU O 205 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU O 205 " --> pdb=" O ARG O 182 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY O 253 " --> pdb=" O TYR O 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS O 249 " --> pdb=" O ALA O 202 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'O' and resid 72 through 75 Processing sheet with id=49, first strand: chain 'O' and resid 106 through 112 removed outlier: 7.107A pdb=" N SER O 106 " --> pdb=" O GLN O 128 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN O 128 " --> pdb=" O SER O 106 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP O 108 " --> pdb=" O THR O 126 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU O 122 " --> pdb=" O GLN O 112 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'O' and resid 236 through 238 removed outlier: 4.099A pdb=" N ALA O 237 " --> pdb=" O LYS O 244 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS O 244 " --> pdb=" O ALA O 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=50 Processing sheet with id=51, first strand: chain 'P' and resid 8 through 18 removed outlier: 5.910A pdb=" N GLN P 8 " --> pdb=" O GLY P 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA P 28 " --> pdb=" O THR P 18 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL P 60 " --> pdb=" O ALA P 44 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER P 46 " --> pdb=" O THR P 58 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR P 58 " --> pdb=" O SER P 46 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS P 112 " --> pdb=" O HIS P 120 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL P 122 " --> pdb=" O MET P 110 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET P 110 " --> pdb=" O VAL P 122 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE P 124 " --> pdb=" O PRO P 108 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N CYS P 126 " --> pdb=" O ASP P 106 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP P 106 " --> pdb=" O CYS P 126 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG P 128 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ARG P 104 " --> pdb=" O ARG P 128 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU P 80 " --> pdb=" O PHE P 103 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'Q' and resid 9 through 10 Processing sheet with id=53, first strand: chain 'Q' and resid 28 through 29 removed outlier: 3.768A pdb=" N VAL Q 43 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL Q 60 " --> pdb=" O ILE Q 46 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N ILE Q 123 " --> pdb=" O MET Q 116 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N MET Q 116 " --> pdb=" O ILE Q 123 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG Q 125 " --> pdb=" O SER Q 114 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N SER Q 114 " --> pdb=" O ARG Q 125 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR Q 127 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS Q 112 " --> pdb=" O THR Q 127 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG Q 129 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY Q 133 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE Q 106 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'Q' and resid 50 through 51 Processing sheet with id=55, first strand: chain 'Q' and resid 94 through 95 Processing sheet with id=56, first strand: chain 'R' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU R 30 " --> pdb=" O ILE R 189 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG R 182 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU R 205 " --> pdb=" O ARG R 182 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR R 226 " --> pdb=" O ASN R 209 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'R' and resid 90 through 91 removed outlier: 4.243A pdb=" N LEU R 30 " --> pdb=" O ILE R 189 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG R 182 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU R 205 " --> pdb=" O ARG R 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY R 253 " --> pdb=" O TYR R 198 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS R 249 " --> pdb=" O ALA R 202 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'R' and resid 72 through 75 Processing sheet with id=59, first strand: chain 'R' and resid 106 through 112 removed outlier: 7.107A pdb=" N SER R 106 " --> pdb=" O GLN R 128 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN R 128 " --> pdb=" O SER R 106 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP R 108 " --> pdb=" O THR R 126 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU R 122 " --> pdb=" O GLN R 112 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'R' and resid 236 through 238 removed outlier: 4.099A pdb=" N ALA R 237 " --> pdb=" O LYS R 244 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS R 244 " --> pdb=" O ALA R 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=60 954 hydrogen bonds defined for protein. 2538 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: 7.99 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8226 1.34 - 1.46: 5363 1.46 - 1.58: 10945 1.58 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 24660 Sorted by residual: bond pdb=" C LYS E 112 " pdb=" N PRO E 113 " ideal model delta sigma weight residual 1.330 1.353 -0.022 1.19e-02 7.06e+03 3.52e+00 bond pdb=" C LYS H 112 " pdb=" N PRO H 113 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.19e-02 7.06e+03 3.43e+00 bond pdb=" C LYS B 112 " pdb=" N PRO B 113 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.19e-02 7.06e+03 3.37e+00 bond pdb=" C LYS K 112 " pdb=" N PRO K 113 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.19e-02 7.06e+03 3.37e+00 bond pdb=" C LYS N 112 " pdb=" N PRO N 113 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.19e-02 7.06e+03 3.33e+00 ... (remaining 24655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 32686 1.59 - 3.17: 766 3.17 - 4.76: 94 4.76 - 6.34: 12 6.34 - 7.93: 6 Bond angle restraints: 33564 Sorted by residual: angle pdb=" N ILE I 247 " pdb=" CA ILE I 247 " pdb=" C ILE I 247 " ideal model delta sigma weight residual 113.53 110.68 2.85 9.80e-01 1.04e+00 8.47e+00 angle pdb=" CA LEU E 38 " pdb=" C LEU E 38 " pdb=" N PRO E 39 " ideal model delta sigma weight residual 120.52 118.10 2.42 8.30e-01 1.45e+00 8.47e+00 angle pdb=" CA LEU Q 38 " pdb=" C LEU Q 38 " pdb=" N PRO Q 39 " ideal model delta sigma weight residual 120.52 118.11 2.41 8.30e-01 1.45e+00 8.45e+00 angle pdb=" CA LEU B 38 " pdb=" C LEU B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 120.52 118.12 2.40 8.30e-01 1.45e+00 8.36e+00 angle pdb=" N ILE C 247 " pdb=" CA ILE C 247 " pdb=" C ILE C 247 " ideal model delta sigma weight residual 113.53 110.70 2.83 9.80e-01 1.04e+00 8.34e+00 ... (remaining 33559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 13308 16.48 - 32.96: 1020 32.96 - 49.43: 198 49.43 - 65.91: 42 65.91 - 82.39: 54 Dihedral angle restraints: 14622 sinusoidal: 5754 harmonic: 8868 Sorted by residual: dihedral pdb=" CG LYS O 211 " pdb=" CD LYS O 211 " pdb=" CE LYS O 211 " pdb=" NZ LYS O 211 " ideal model delta sinusoidal sigma weight residual -60.00 -117.48 57.48 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG LYS C 211 " pdb=" CD LYS C 211 " pdb=" CE LYS C 211 " pdb=" NZ LYS C 211 " ideal model delta sinusoidal sigma weight residual -60.00 -117.47 57.47 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG LYS L 211 " pdb=" CD LYS L 211 " pdb=" CE LYS L 211 " pdb=" NZ LYS L 211 " ideal model delta sinusoidal sigma weight residual -60.00 -117.46 57.46 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 14619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2241 0.026 - 0.053: 836 0.053 - 0.079: 231 0.079 - 0.105: 245 0.105 - 0.132: 53 Chirality restraints: 3606 Sorted by residual: chirality pdb=" CA VAL M 20 " pdb=" N VAL M 20 " pdb=" C VAL M 20 " pdb=" CB VAL M 20 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA VAL G 20 " pdb=" N VAL G 20 " pdb=" C VAL G 20 " pdb=" CB VAL G 20 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL H 139 " pdb=" N VAL H 139 " pdb=" C VAL H 139 " pdb=" CB VAL H 139 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 3603 not shown) Planarity restraints: 4518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 112 " -0.027 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 113 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 112 " -0.027 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO Q 113 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO Q 113 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO Q 113 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 112 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO H 113 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO H 113 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 113 " 0.023 5.00e-02 4.00e+02 ... (remaining 4515 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.84: 48 1.84 - 2.60: 426 2.60 - 3.37: 29408 3.37 - 4.13: 55185 4.13 - 4.90: 101214 Nonbonded interactions: 186281 Sorted by model distance: nonbonded pdb=" CD GLN C 61 " pdb=" CD2 LEU F 5 " model vdw 1.070 3.690 nonbonded pdb=" CD GLN I 61 " pdb=" CD2 LEU L 5 " model vdw 1.071 3.690 nonbonded pdb=" CD2 LEU C 5 " pdb=" CD GLN R 61 " model vdw 1.071 3.690 nonbonded pdb=" CD GLN F 61 " pdb=" CD2 LEU I 5 " model vdw 1.071 3.690 nonbonded pdb=" CD GLN L 61 " pdb=" CD2 LEU O 5 " model vdw 1.071 3.690 ... (remaining 186276 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: 0.21 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.050 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 48.520 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.009 0.574 24666 Z= 0.906 Angle : 0.573 7.928 33564 Z= 0.327 Chirality : 0.039 0.132 3606 Planarity : 0.005 0.042 4518 Dihedral : 13.211 82.388 8958 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3090 helix: 1.46 (0.27), residues: 378 sheet: 0.60 (0.16), residues: 1038 loop : -0.60 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 21 HIS 0.002 0.001 HIS G 40 PHE 0.011 0.001 PHE K 88 TYR 0.012 0.001 TYR I 198 ARG 0.004 0.001 ARG B 89 Details of bonding type rmsd hydrogen bonds : bond 0.25869 ( 840) hydrogen bonds : angle 8.92969 ( 2538) covalent geometry : bond 0.00274 (24660) covalent geometry : angle 0.57294 (33564) Misc. bond : bond 0.57350 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 674 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8339 (mttt) REVERT: B 15 GLU cc_start: 0.8151 (mp0) cc_final: 0.7721 (mp0) REVERT: B 40 PHE cc_start: 0.8295 (t80) cc_final: 0.7428 (t80) REVERT: B 89 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8395 (mmm160) REVERT: B 131 GLN cc_start: 0.9113 (tt0) cc_final: 0.8906 (tt0) REVERT: C 125 ILE cc_start: 0.8620 (mm) cc_final: 0.7939 (tp) REVERT: C 199 GLU cc_start: 0.8105 (tt0) cc_final: 0.7735 (tm-30) REVERT: C 236 MET cc_start: 0.8056 (mmt) cc_final: 0.7019 (mmm) REVERT: D 4 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7933 (mp0) REVERT: D 53 GLN cc_start: 0.7637 (mt0) cc_final: 0.7408 (mt0) REVERT: D 112 LYS cc_start: 0.8977 (mmtt) cc_final: 0.8371 (mttt) REVERT: D 113 TYR cc_start: 0.8775 (m-80) cc_final: 0.8502 (m-80) REVERT: E 78 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8181 (mtpp) REVERT: E 89 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8407 (mmm160) REVERT: E 127 THR cc_start: 0.9417 (m) cc_final: 0.9022 (p) REVERT: F 125 ILE cc_start: 0.8895 (mm) cc_final: 0.8408 (mm) REVERT: F 199 GLU cc_start: 0.7946 (tt0) cc_final: 0.7728 (tm-30) REVERT: F 226 THR cc_start: 0.8689 (m) cc_final: 0.8033 (p) REVERT: G 17 GLU cc_start: 0.9082 (pp20) cc_final: 0.8870 (pp20) REVERT: G 112 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8341 (mttt) REVERT: H 14 GLU cc_start: 0.7677 (pm20) cc_final: 0.7460 (pm20) REVERT: H 15 GLU cc_start: 0.7875 (mp0) cc_final: 0.7040 (mp0) REVERT: H 78 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8170 (mtpp) REVERT: H 127 THR cc_start: 0.9473 (m) cc_final: 0.9165 (p) REVERT: H 129 ARG cc_start: 0.8572 (ttm170) cc_final: 0.8371 (ttm170) REVERT: H 136 TYR cc_start: 0.8370 (m-80) cc_final: 0.8110 (m-80) REVERT: I 114 ILE cc_start: 0.8544 (mm) cc_final: 0.8295 (tp) REVERT: I 125 ILE cc_start: 0.8933 (mm) cc_final: 0.8374 (tp) REVERT: I 244 LYS cc_start: 0.8829 (pttt) cc_final: 0.8505 (pttm) REVERT: J 63 LEU cc_start: 0.9104 (tt) cc_final: 0.8897 (tt) REVERT: J 112 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8308 (mttt) REVERT: K 40 PHE cc_start: 0.8279 (t80) cc_final: 0.7393 (t80) REVERT: K 78 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8276 (mtpp) REVERT: K 89 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8406 (mmm160) REVERT: K 131 GLN cc_start: 0.9117 (tt0) cc_final: 0.8909 (tt0) REVERT: L 125 ILE cc_start: 0.8633 (mm) cc_final: 0.7972 (tp) REVERT: L 236 MET cc_start: 0.8072 (mmt) cc_final: 0.7438 (mmp) REVERT: M 4 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7893 (mp0) REVERT: M 53 GLN cc_start: 0.7630 (mt0) cc_final: 0.7391 (mt0) REVERT: M 112 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8347 (mttt) REVERT: M 113 TYR cc_start: 0.8766 (m-80) cc_final: 0.8510 (m-80) REVERT: N 78 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8192 (mtpp) REVERT: N 89 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8444 (mmm160) REVERT: N 127 THR cc_start: 0.9424 (m) cc_final: 0.9030 (p) REVERT: O 125 ILE cc_start: 0.8834 (mm) cc_final: 0.8370 (mm) REVERT: O 199 GLU cc_start: 0.7947 (tt0) cc_final: 0.7722 (tm-30) REVERT: O 226 THR cc_start: 0.8680 (m) cc_final: 0.8018 (p) REVERT: O 236 MET cc_start: 0.8381 (mmt) cc_final: 0.8178 (mmm) REVERT: P 112 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8306 (mttt) REVERT: P 113 TYR cc_start: 0.8837 (m-80) cc_final: 0.8629 (m-80) REVERT: Q 14 GLU cc_start: 0.7617 (pm20) cc_final: 0.7416 (pm20) REVERT: Q 15 GLU cc_start: 0.7861 (mp0) cc_final: 0.7038 (mp0) REVERT: Q 78 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8171 (mtpp) REVERT: Q 127 THR cc_start: 0.9469 (m) cc_final: 0.9179 (p) REVERT: R 114 ILE cc_start: 0.8533 (mm) cc_final: 0.8277 (tp) REVERT: R 125 ILE cc_start: 0.8919 (mm) cc_final: 0.8352 (tp) REVERT: R 244 LYS cc_start: 0.8780 (pttt) cc_final: 0.8510 (pttm) outliers start: 0 outliers final: 0 residues processed: 674 average time/residue: 0.3834 time to fit residues: 386.1570 Evaluate side-chains 515 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 142 optimal weight: 0.0570 chunk 175 optimal weight: 0.4980 chunk 272 optimal weight: 10.0000 overall best weight: 4.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN C 209 ASN F 86 ASN F 138 GLN F 209 ASN I 86 ASN I 138 GLN I 150 ASN I 209 ASN L 86 ASN L 209 ASN O 86 ASN O 138 GLN O 209 ASN R 86 ASN R 138 GLN R 150 ASN R 209 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.064654 restraints weight = 66312.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.066781 restraints weight = 32539.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068204 restraints weight = 20089.035| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24666 Z= 0.218 Angle : 0.614 7.920 33564 Z= 0.312 Chirality : 0.042 0.164 3606 Planarity : 0.005 0.045 4518 Dihedral : 3.879 16.607 3372 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.37 % Allowed : 9.64 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3090 helix: 0.67 (0.25), residues: 426 sheet: 0.53 (0.16), residues: 1032 loop : -0.73 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 23 HIS 0.003 0.001 HIS D 40 PHE 0.015 0.002 PHE I 121 TYR 0.015 0.002 TYR G 113 ARG 0.004 0.001 ARG N 89 Details of bonding type rmsd hydrogen bonds : bond 0.05123 ( 840) hydrogen bonds : angle 6.16789 ( 2538) covalent geometry : bond 0.00494 (24660) covalent geometry : angle 0.61361 (33564) Misc. bond : bond 0.00294 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 510 time to evaluate : 2.660 Fit side-chains REVERT: A 55 ASN cc_start: 0.9216 (m-40) cc_final: 0.8859 (m-40) REVERT: A 99 ARG cc_start: 0.8721 (mtp85) cc_final: 0.8350 (mtt90) REVERT: A 112 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8409 (mttt) REVERT: B 37 GLU cc_start: 0.8266 (pm20) cc_final: 0.7963 (pm20) REVERT: B 40 PHE cc_start: 0.8421 (t80) cc_final: 0.7939 (t80) REVERT: B 78 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8285 (mtpp) REVERT: C 114 ILE cc_start: 0.8813 (mm) cc_final: 0.8593 (tp) REVERT: C 125 ILE cc_start: 0.9015 (mm) cc_final: 0.8814 (mm) REVERT: C 215 LYS cc_start: 0.9543 (tttt) cc_final: 0.9300 (tttm) REVERT: C 236 MET cc_start: 0.8276 (mmt) cc_final: 0.7636 (mmt) REVERT: D 55 ASN cc_start: 0.9139 (m-40) cc_final: 0.8795 (m-40) REVERT: D 112 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8528 (mttt) REVERT: D 127 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8646 (ttpt) REVERT: E 15 GLU cc_start: 0.8169 (mp0) cc_final: 0.7884 (mp0) REVERT: E 78 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8256 (mtpp) REVERT: E 127 THR cc_start: 0.9379 (m) cc_final: 0.9050 (p) REVERT: F 213 GLU cc_start: 0.8462 (tt0) cc_final: 0.8238 (tt0) REVERT: F 226 THR cc_start: 0.8939 (m) cc_final: 0.8513 (p) REVERT: F 236 MET cc_start: 0.8486 (mmm) cc_final: 0.7721 (mmm) REVERT: G 79 GLU cc_start: 0.8243 (mp0) cc_final: 0.7708 (mp0) REVERT: G 112 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8427 (mttt) REVERT: H 14 GLU cc_start: 0.7837 (pm20) cc_final: 0.7507 (pm20) REVERT: H 15 GLU cc_start: 0.7925 (mp0) cc_final: 0.7131 (mp0) REVERT: H 46 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8672 (mt) REVERT: H 78 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8231 (mtpp) REVERT: I 113 MET cc_start: 0.8049 (mmm) cc_final: 0.7784 (mmp) REVERT: I 215 LYS cc_start: 0.9604 (tttt) cc_final: 0.9258 (tttm) REVERT: J 55 ASN cc_start: 0.9205 (m-40) cc_final: 0.8853 (m-40) REVERT: J 99 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8329 (mtt90) REVERT: J 112 LYS cc_start: 0.9227 (mmtt) cc_final: 0.8402 (mttt) REVERT: K 37 GLU cc_start: 0.8224 (pm20) cc_final: 0.7892 (pm20) REVERT: K 40 PHE cc_start: 0.8421 (t80) cc_final: 0.7947 (t80) REVERT: K 78 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8314 (mtpp) REVERT: L 114 ILE cc_start: 0.8809 (mm) cc_final: 0.8572 (tp) REVERT: L 125 ILE cc_start: 0.9016 (mm) cc_final: 0.8799 (mm) REVERT: L 215 LYS cc_start: 0.9541 (tttt) cc_final: 0.9293 (tttm) REVERT: L 224 GLU cc_start: 0.7629 (pm20) cc_final: 0.7428 (pm20) REVERT: L 236 MET cc_start: 0.8317 (mmt) cc_final: 0.7698 (mmt) REVERT: M 55 ASN cc_start: 0.9139 (m-40) cc_final: 0.8781 (m-40) REVERT: M 112 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8505 (mttt) REVERT: M 127 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8648 (ttpt) REVERT: N 78 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8224 (mtpp) REVERT: N 127 THR cc_start: 0.9375 (m) cc_final: 0.9043 (p) REVERT: O 213 GLU cc_start: 0.8458 (tt0) cc_final: 0.8237 (tt0) REVERT: O 226 THR cc_start: 0.8938 (m) cc_final: 0.8497 (p) REVERT: P 79 GLU cc_start: 0.8236 (mp0) cc_final: 0.7749 (mp0) REVERT: P 112 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8408 (mttt) REVERT: Q 14 GLU cc_start: 0.7828 (pm20) cc_final: 0.7514 (pm20) REVERT: Q 15 GLU cc_start: 0.7913 (mp0) cc_final: 0.7139 (mp0) REVERT: Q 46 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8679 (mt) REVERT: Q 78 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8232 (mtpp) REVERT: R 215 LYS cc_start: 0.9600 (tttt) cc_final: 0.9254 (tttm) outliers start: 34 outliers final: 12 residues processed: 531 average time/residue: 0.3992 time to fit residues: 318.4659 Evaluate side-chains 489 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 475 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 134 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 291 optimal weight: 0.4980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN I 150 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.075681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.064997 restraints weight = 65790.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.067150 restraints weight = 32329.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.068605 restraints weight = 19925.970| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24666 Z= 0.176 Angle : 0.583 9.093 33564 Z= 0.292 Chirality : 0.040 0.149 3606 Planarity : 0.005 0.049 4518 Dihedral : 3.872 15.944 3372 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.53 % Allowed : 11.29 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3090 helix: 0.84 (0.25), residues: 426 sheet: 0.54 (0.16), residues: 1032 loop : -0.79 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 23 HIS 0.003 0.001 HIS C 72 PHE 0.013 0.001 PHE F 121 TYR 0.017 0.001 TYR O 243 ARG 0.005 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 840) hydrogen bonds : angle 5.67685 ( 2538) covalent geometry : bond 0.00403 (24660) covalent geometry : angle 0.58304 (33564) Misc. bond : bond 0.00276 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 493 time to evaluate : 2.640 Fit side-chains REVERT: A 55 ASN cc_start: 0.9273 (m-40) cc_final: 0.8930 (m-40) REVERT: A 112 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8420 (mttt) REVERT: A 125 MET cc_start: 0.8845 (mmm) cc_final: 0.8528 (tpp) REVERT: A 127 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8879 (ttmt) REVERT: B 15 GLU cc_start: 0.8207 (mp0) cc_final: 0.7993 (mp0) REVERT: B 31 GLU cc_start: 0.8102 (tp30) cc_final: 0.7701 (tp30) REVERT: B 40 PHE cc_start: 0.8494 (t80) cc_final: 0.8033 (t80) REVERT: B 78 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8306 (mtpp) REVERT: C 114 ILE cc_start: 0.8825 (mm) cc_final: 0.8565 (tp) REVERT: C 124 ASP cc_start: 0.8661 (t0) cc_final: 0.8414 (t0) REVERT: C 125 ILE cc_start: 0.9205 (mm) cc_final: 0.8903 (pt) REVERT: C 198 TYR cc_start: 0.9171 (m-80) cc_final: 0.8703 (m-80) REVERT: C 215 LYS cc_start: 0.9573 (tttt) cc_final: 0.9296 (tttm) REVERT: C 236 MET cc_start: 0.8378 (mmt) cc_final: 0.7594 (mmp) REVERT: D 55 ASN cc_start: 0.9179 (m-40) cc_final: 0.8805 (m-40) REVERT: D 112 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8494 (mttt) REVERT: D 127 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8558 (ttmt) REVERT: E 57 ASP cc_start: 0.8079 (t0) cc_final: 0.7811 (m-30) REVERT: E 78 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8239 (mtpp) REVERT: F 213 GLU cc_start: 0.8455 (tt0) cc_final: 0.8132 (tt0) REVERT: F 215 LYS cc_start: 0.9633 (tttt) cc_final: 0.9427 (tttm) REVERT: F 226 THR cc_start: 0.8987 (m) cc_final: 0.8722 (p) REVERT: F 236 MET cc_start: 0.8410 (mmm) cc_final: 0.7956 (mmm) REVERT: G 79 GLU cc_start: 0.8182 (mp0) cc_final: 0.7650 (mp0) REVERT: G 112 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8520 (mttt) REVERT: H 14 GLU cc_start: 0.7892 (pm20) cc_final: 0.7632 (pm20) REVERT: H 15 GLU cc_start: 0.7734 (mp0) cc_final: 0.7476 (mp0) REVERT: H 78 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8196 (mtpp) REVERT: H 84 MET cc_start: 0.9389 (mmp) cc_final: 0.9181 (mmt) REVERT: I 215 LYS cc_start: 0.9651 (tttt) cc_final: 0.9350 (tttm) REVERT: J 55 ASN cc_start: 0.9262 (m-40) cc_final: 0.8920 (m-40) REVERT: J 112 LYS cc_start: 0.9221 (mmtt) cc_final: 0.8406 (mttt) REVERT: J 125 MET cc_start: 0.8832 (mmm) cc_final: 0.8550 (tpp) REVERT: J 127 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8886 (ttmt) REVERT: K 40 PHE cc_start: 0.8492 (t80) cc_final: 0.8030 (t80) REVERT: K 78 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8277 (mtpp) REVERT: L 125 ILE cc_start: 0.9135 (mm) cc_final: 0.8904 (pt) REVERT: L 176 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8063 (p0) REVERT: L 198 TYR cc_start: 0.9165 (m-80) cc_final: 0.8710 (m-80) REVERT: L 215 LYS cc_start: 0.9573 (tttt) cc_final: 0.9290 (tttm) REVERT: L 236 MET cc_start: 0.8353 (mmt) cc_final: 0.7543 (mmp) REVERT: M 55 ASN cc_start: 0.9178 (m-40) cc_final: 0.8821 (m-40) REVERT: M 112 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8475 (mttt) REVERT: M 127 LYS cc_start: 0.8961 (ttmm) cc_final: 0.8488 (ttmt) REVERT: N 57 ASP cc_start: 0.8071 (t0) cc_final: 0.7786 (m-30) REVERT: N 78 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8292 (mtpp) REVERT: O 213 GLU cc_start: 0.8457 (tt0) cc_final: 0.8134 (tt0) REVERT: O 215 LYS cc_start: 0.9629 (tttt) cc_final: 0.9426 (tttm) REVERT: O 226 THR cc_start: 0.8978 (m) cc_final: 0.8708 (p) REVERT: O 236 MET cc_start: 0.8427 (mmm) cc_final: 0.7841 (mmm) REVERT: P 79 GLU cc_start: 0.8256 (mp0) cc_final: 0.7621 (mp0) REVERT: P 112 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8531 (mttt) REVERT: Q 78 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8249 (mtpp) REVERT: Q 84 MET cc_start: 0.9398 (mmp) cc_final: 0.9189 (mmt) REVERT: R 113 MET cc_start: 0.8167 (mmm) cc_final: 0.7911 (mmp) REVERT: R 215 LYS cc_start: 0.9653 (tttt) cc_final: 0.9356 (tttm) outliers start: 38 outliers final: 26 residues processed: 511 average time/residue: 0.4149 time to fit residues: 322.2578 Evaluate side-chains 493 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 466 time to evaluate : 2.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 56 optimal weight: 0.0870 chunk 135 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 240 optimal weight: 0.0170 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.076815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.066134 restraints weight = 66106.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068293 restraints weight = 32456.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.069779 restraints weight = 19942.360| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24666 Z= 0.124 Angle : 0.576 13.415 33564 Z= 0.285 Chirality : 0.040 0.141 3606 Planarity : 0.004 0.050 4518 Dihedral : 3.767 14.538 3372 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.01 % Allowed : 11.97 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3090 helix: 0.89 (0.26), residues: 426 sheet: 0.51 (0.16), residues: 1044 loop : -0.79 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 23 HIS 0.002 0.001 HIS C 72 PHE 0.009 0.001 PHE F 121 TYR 0.017 0.001 TYR R 243 ARG 0.006 0.000 ARG R 27 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 840) hydrogen bonds : angle 5.44930 ( 2538) covalent geometry : bond 0.00286 (24660) covalent geometry : angle 0.57632 (33564) Misc. bond : bond 0.00573 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 486 time to evaluate : 2.552 Fit side-chains REVERT: A 55 ASN cc_start: 0.9260 (m-40) cc_final: 0.8922 (m-40) REVERT: A 99 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8396 (mtt90) REVERT: A 112 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8399 (mttt) REVERT: A 125 MET cc_start: 0.8837 (mmm) cc_final: 0.8460 (tpp) REVERT: B 40 PHE cc_start: 0.8473 (t80) cc_final: 0.7994 (t80) REVERT: B 57 ASP cc_start: 0.8030 (m-30) cc_final: 0.7748 (t0) REVERT: B 78 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8399 (mtpp) REVERT: C 124 ASP cc_start: 0.8605 (t0) cc_final: 0.8379 (t0) REVERT: C 125 ILE cc_start: 0.9187 (mm) cc_final: 0.8794 (pt) REVERT: C 198 TYR cc_start: 0.9217 (m-80) cc_final: 0.8910 (m-80) REVERT: C 215 LYS cc_start: 0.9581 (tttt) cc_final: 0.9341 (tttm) REVERT: C 236 MET cc_start: 0.8443 (mmt) cc_final: 0.7786 (mmt) REVERT: D 55 ASN cc_start: 0.9168 (m-40) cc_final: 0.8798 (m-40) REVERT: D 112 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8510 (mttt) REVERT: D 127 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8596 (ttmt) REVERT: E 14 GLU cc_start: 0.7904 (pm20) cc_final: 0.7628 (pm20) REVERT: E 15 GLU cc_start: 0.7947 (mp0) cc_final: 0.7693 (mp0) REVERT: E 37 GLU cc_start: 0.8232 (pm20) cc_final: 0.7858 (mp0) REVERT: E 57 ASP cc_start: 0.7994 (t0) cc_final: 0.7745 (m-30) REVERT: E 78 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8214 (mtpp) REVERT: F 124 ASP cc_start: 0.8568 (t0) cc_final: 0.7813 (m-30) REVERT: F 215 LYS cc_start: 0.9643 (tttt) cc_final: 0.9355 (tttm) REVERT: F 226 THR cc_start: 0.8922 (m) cc_final: 0.8673 (p) REVERT: F 236 MET cc_start: 0.8365 (mmm) cc_final: 0.8016 (mmm) REVERT: G 79 GLU cc_start: 0.8211 (mp0) cc_final: 0.7360 (mp0) REVERT: G 112 LYS cc_start: 0.9117 (mmtt) cc_final: 0.8500 (mttt) REVERT: H 14 GLU cc_start: 0.7894 (pm20) cc_final: 0.7661 (pm20) REVERT: H 47 ASP cc_start: 0.8053 (m-30) cc_final: 0.7847 (m-30) REVERT: H 78 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8169 (mtpp) REVERT: H 108 GLU cc_start: 0.7836 (tt0) cc_final: 0.7494 (mt-10) REVERT: I 215 LYS cc_start: 0.9579 (tttt) cc_final: 0.9294 (tttm) REVERT: I 236 MET cc_start: 0.8683 (mmm) cc_final: 0.8471 (mmp) REVERT: J 55 ASN cc_start: 0.9245 (m-40) cc_final: 0.8915 (m-40) REVERT: J 99 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8405 (mtt90) REVERT: J 112 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8388 (mttt) REVERT: J 125 MET cc_start: 0.8864 (mmm) cc_final: 0.8507 (tpp) REVERT: K 40 PHE cc_start: 0.8464 (t80) cc_final: 0.7983 (t80) REVERT: K 78 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8340 (mtpp) REVERT: L 176 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8122 (p0) REVERT: L 198 TYR cc_start: 0.9161 (m-80) cc_final: 0.8868 (m-80) REVERT: L 215 LYS cc_start: 0.9581 (tttt) cc_final: 0.9335 (tttm) REVERT: L 236 MET cc_start: 0.8488 (mmt) cc_final: 0.7850 (mmt) REVERT: M 55 ASN cc_start: 0.9162 (m-40) cc_final: 0.8790 (m-40) REVERT: M 112 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8501 (mttt) REVERT: M 127 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8609 (ttmt) REVERT: N 14 GLU cc_start: 0.7962 (pm20) cc_final: 0.7672 (pm20) REVERT: N 15 GLU cc_start: 0.8111 (mp0) cc_final: 0.7849 (mp0) REVERT: N 57 ASP cc_start: 0.7972 (t0) cc_final: 0.7734 (m-30) REVERT: N 78 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8207 (mtpp) REVERT: O 215 LYS cc_start: 0.9642 (tttt) cc_final: 0.9356 (tttm) REVERT: O 226 THR cc_start: 0.8911 (m) cc_final: 0.8666 (p) REVERT: O 236 MET cc_start: 0.8376 (mmm) cc_final: 0.7943 (mmm) REVERT: P 79 GLU cc_start: 0.8240 (mp0) cc_final: 0.7552 (mp0) REVERT: P 112 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8477 (mttt) REVERT: Q 15 GLU cc_start: 0.7791 (mp0) cc_final: 0.7539 (mp0) REVERT: Q 47 ASP cc_start: 0.7927 (m-30) cc_final: 0.7608 (m-30) REVERT: Q 78 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8247 (mtpp) REVERT: R 113 MET cc_start: 0.8145 (mmm) cc_final: 0.7876 (mmp) REVERT: R 215 LYS cc_start: 0.9582 (tttt) cc_final: 0.9297 (tttm) REVERT: R 236 MET cc_start: 0.8679 (mmm) cc_final: 0.8469 (mmp) outliers start: 50 outliers final: 37 residues processed: 517 average time/residue: 0.3694 time to fit residues: 290.7991 Evaluate side-chains 515 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 477 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 56 THR Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 15 optimal weight: 0.0470 chunk 292 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 ASN ** 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 = 0.2943 r_free = 0.2943 target = 0.073337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.062964 restraints weight = 67765.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.065018 restraints weight = 33133.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.066427 restraints weight = 20290.226| |-----------------------------------------------------------------------------| r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 24666 Z= 0.294 Angle : 0.671 11.430 33564 Z= 0.336 Chirality : 0.042 0.160 3606 Planarity : 0.005 0.049 4518 Dihedral : 4.182 17.712 3372 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.97 % Allowed : 12.05 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 3090 helix: 0.62 (0.25), residues: 426 sheet: 0.31 (0.16), residues: 1044 loop : -0.94 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 23 HIS 0.006 0.001 HIS N 120 PHE 0.024 0.002 PHE I 121 TYR 0.022 0.002 TYR R 198 ARG 0.004 0.001 ARG O 104 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 840) hydrogen bonds : angle 5.47487 ( 2538) covalent geometry : bond 0.00668 (24660) covalent geometry : angle 0.67148 (33564) Misc. bond : bond 0.00567 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 460 time to evaluate : 2.477 Fit side-chains revert: symmetry clash REVERT: A 18 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8537 (m) REVERT: A 55 ASN cc_start: 0.9286 (m-40) cc_final: 0.8896 (m-40) REVERT: A 99 ARG cc_start: 0.8761 (mtp85) cc_final: 0.8467 (mtt90) REVERT: A 112 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8463 (mttt) REVERT: A 125 MET cc_start: 0.8825 (mmm) cc_final: 0.8536 (tpp) REVERT: B 40 PHE cc_start: 0.8513 (t80) cc_final: 0.7984 (t80) REVERT: B 78 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8338 (mtpp) REVERT: C 125 ILE cc_start: 0.9172 (mm) cc_final: 0.8939 (pt) REVERT: C 236 MET cc_start: 0.8568 (mmt) cc_final: 0.7832 (mmt) REVERT: D 55 ASN cc_start: 0.9175 (m-40) cc_final: 0.8804 (m-40) REVERT: D 112 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8509 (mttt) REVERT: E 14 GLU cc_start: 0.7946 (pm20) cc_final: 0.7645 (pm20) REVERT: E 37 GLU cc_start: 0.8263 (pm20) cc_final: 0.8033 (pm20) REVERT: E 57 ASP cc_start: 0.8020 (t0) cc_final: 0.7661 (t0) REVERT: E 78 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8290 (mtpp) REVERT: F 213 GLU cc_start: 0.8565 (tt0) cc_final: 0.8340 (tt0) REVERT: F 215 LYS cc_start: 0.9662 (tttt) cc_final: 0.9367 (tttm) REVERT: F 236 MET cc_start: 0.8477 (mmm) cc_final: 0.8222 (mmm) REVERT: F 238 MET cc_start: 0.8631 (tpp) cc_final: 0.8339 (tpp) REVERT: G 18 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.7883 (m) REVERT: G 79 GLU cc_start: 0.8254 (mp0) cc_final: 0.7447 (mp0) REVERT: G 112 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8481 (mttt) REVERT: H 47 ASP cc_start: 0.8117 (m-30) cc_final: 0.7803 (m-30) REVERT: H 78 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8210 (mtpp) REVERT: I 215 LYS cc_start: 0.9658 (tttt) cc_final: 0.9393 (tttm) REVERT: J 18 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8522 (m) REVERT: J 55 ASN cc_start: 0.9279 (m-40) cc_final: 0.8897 (m-40) REVERT: J 99 ARG cc_start: 0.8766 (mtp85) cc_final: 0.8459 (mtt90) REVERT: J 112 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8460 (mttt) REVERT: J 125 MET cc_start: 0.8818 (mmm) cc_final: 0.8547 (tpp) REVERT: K 31 GLU cc_start: 0.8061 (tp30) cc_final: 0.7811 (tp30) REVERT: K 40 PHE cc_start: 0.8498 (t80) cc_final: 0.7968 (t80) REVERT: K 78 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8347 (mtpp) REVERT: L 125 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8877 (pt) REVERT: L 198 TYR cc_start: 0.9226 (m-80) cc_final: 0.8977 (m-80) REVERT: L 215 LYS cc_start: 0.9655 (tttt) cc_final: 0.9429 (tttm) REVERT: L 236 MET cc_start: 0.8570 (mmt) cc_final: 0.7849 (mmt) REVERT: M 55 ASN cc_start: 0.9184 (m-40) cc_final: 0.8819 (m-40) REVERT: M 112 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8502 (mttt) REVERT: N 14 GLU cc_start: 0.7941 (pm20) cc_final: 0.7741 (pm20) REVERT: N 15 GLU cc_start: 0.8148 (mp0) cc_final: 0.7732 (mp0) REVERT: N 37 GLU cc_start: 0.8268 (pm20) cc_final: 0.8052 (pm20) REVERT: N 78 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8292 (mtpp) REVERT: O 213 GLU cc_start: 0.8523 (tt0) cc_final: 0.8288 (tt0) REVERT: O 215 LYS cc_start: 0.9665 (tttt) cc_final: 0.9367 (tttm) REVERT: O 236 MET cc_start: 0.8507 (mmm) cc_final: 0.8154 (mmm) REVERT: O 238 MET cc_start: 0.8679 (tpp) cc_final: 0.8441 (tpp) REVERT: P 18 THR cc_start: 0.8452 (OUTLIER) cc_final: 0.7873 (m) REVERT: P 79 GLU cc_start: 0.8266 (mp0) cc_final: 0.7428 (mp0) REVERT: P 112 LYS cc_start: 0.9175 (mmtt) cc_final: 0.8421 (mttt) REVERT: Q 14 GLU cc_start: 0.7820 (pm20) cc_final: 0.7488 (pm20) REVERT: Q 15 GLU cc_start: 0.7650 (mp0) cc_final: 0.7419 (mp0) REVERT: Q 47 ASP cc_start: 0.8032 (m-30) cc_final: 0.7739 (m-30) REVERT: Q 78 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8207 (mtpp) REVERT: R 215 LYS cc_start: 0.9656 (tttt) cc_final: 0.9393 (tttm) outliers start: 74 outliers final: 52 residues processed: 494 average time/residue: 0.3805 time to fit residues: 284.9186 Evaluate side-chains 494 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 437 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 162 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 234 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN F 209 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN O 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.074982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.064480 restraints weight = 66184.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.066576 restraints weight = 32348.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.068005 restraints weight = 19861.945| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24666 Z= 0.136 Angle : 0.612 13.390 33564 Z= 0.299 Chirality : 0.040 0.155 3606 Planarity : 0.004 0.052 4518 Dihedral : 3.926 16.054 3372 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.85 % Allowed : 14.50 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3090 helix: 0.88 (0.25), residues: 426 sheet: 0.32 (0.16), residues: 1050 loop : -0.83 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 23 HIS 0.004 0.001 HIS B 81 PHE 0.011 0.001 PHE F 121 TYR 0.022 0.001 TYR G 113 ARG 0.003 0.000 ARG O 27 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 840) hydrogen bonds : angle 5.23218 ( 2538) covalent geometry : bond 0.00310 (24660) covalent geometry : angle 0.61246 (33564) Misc. bond : bond 0.00823 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 465 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.9296 (m-40) cc_final: 0.8956 (m-40) REVERT: A 99 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8402 (mtt90) REVERT: A 112 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8426 (mttt) REVERT: A 125 MET cc_start: 0.8780 (mmm) cc_final: 0.8516 (tpp) REVERT: B 40 PHE cc_start: 0.8481 (t80) cc_final: 0.7913 (t80) REVERT: B 78 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8320 (mtpp) REVERT: C 125 ILE cc_start: 0.9203 (mm) cc_final: 0.8986 (pt) REVERT: C 198 TYR cc_start: 0.9177 (m-80) cc_final: 0.8969 (m-80) REVERT: D 18 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8357 (m) REVERT: D 55 ASN cc_start: 0.9185 (m-40) cc_final: 0.8791 (m-40) REVERT: D 112 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8516 (mttt) REVERT: E 15 GLU cc_start: 0.8258 (mp0) cc_final: 0.7822 (mp0) REVERT: E 37 GLU cc_start: 0.8240 (pm20) cc_final: 0.7922 (mp0) REVERT: E 57 ASP cc_start: 0.7994 (t0) cc_final: 0.7638 (t0) REVERT: E 78 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8255 (mtpp) REVERT: F 215 LYS cc_start: 0.9653 (tttt) cc_final: 0.9351 (tttm) REVERT: F 236 MET cc_start: 0.8629 (mmm) cc_final: 0.8329 (mmm) REVERT: F 238 MET cc_start: 0.8542 (tpp) cc_final: 0.8160 (tpp) REVERT: G 17 GLU cc_start: 0.9085 (pp20) cc_final: 0.8859 (pp20) REVERT: G 79 GLU cc_start: 0.8220 (mp0) cc_final: 0.7565 (mp0) REVERT: G 112 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8544 (mttt) REVERT: H 15 GLU cc_start: 0.8141 (mp0) cc_final: 0.7915 (mp0) REVERT: H 78 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8280 (mtpp) REVERT: I 215 LYS cc_start: 0.9663 (tttt) cc_final: 0.9374 (tttm) REVERT: J 55 ASN cc_start: 0.9286 (m-40) cc_final: 0.8940 (m-40) REVERT: J 99 ARG cc_start: 0.8712 (mtp85) cc_final: 0.8414 (mtt90) REVERT: J 112 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8434 (mttt) REVERT: J 125 MET cc_start: 0.8787 (mmm) cc_final: 0.8507 (tpp) REVERT: K 31 GLU cc_start: 0.7873 (tp30) cc_final: 0.7666 (tp30) REVERT: K 40 PHE cc_start: 0.8471 (t80) cc_final: 0.7908 (t80) REVERT: K 78 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8274 (mtpp) REVERT: L 198 TYR cc_start: 0.9174 (m-80) cc_final: 0.8969 (m-80) REVERT: L 215 LYS cc_start: 0.9637 (tttt) cc_final: 0.9398 (tttm) REVERT: M 18 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8348 (m) REVERT: M 55 ASN cc_start: 0.9177 (m-40) cc_final: 0.8784 (m-40) REVERT: M 112 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8495 (mttt) REVERT: N 14 GLU cc_start: 0.7990 (pm20) cc_final: 0.7787 (pm20) REVERT: N 15 GLU cc_start: 0.8296 (mp0) cc_final: 0.7864 (mp0) REVERT: N 37 GLU cc_start: 0.8234 (pm20) cc_final: 0.7919 (mp0) REVERT: N 57 ASP cc_start: 0.7808 (t0) cc_final: 0.7590 (t0) REVERT: N 78 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8256 (mtpp) REVERT: O 215 LYS cc_start: 0.9650 (tttt) cc_final: 0.9344 (tttm) REVERT: O 236 MET cc_start: 0.8508 (mmm) cc_final: 0.8252 (mmm) REVERT: O 238 MET cc_start: 0.8605 (tpp) cc_final: 0.8259 (tpp) REVERT: P 17 GLU cc_start: 0.9091 (pp20) cc_final: 0.8834 (pp20) REVERT: P 18 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.7870 (m) REVERT: P 79 GLU cc_start: 0.8222 (mp0) cc_final: 0.7960 (mt-10) REVERT: P 112 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8521 (mttt) REVERT: Q 78 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8278 (mtpp) REVERT: R 215 LYS cc_start: 0.9663 (tttt) cc_final: 0.9373 (tttm) outliers start: 46 outliers final: 32 residues processed: 493 average time/residue: 0.3593 time to fit residues: 268.1428 Evaluate side-chains 496 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 461 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain P residue 113 TYR Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 249 optimal weight: 9.9990 chunk 220 optimal weight: 0.0050 chunk 41 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 297 optimal weight: 0.8980 chunk 299 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 ASN F 86 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN R 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.064503 restraints weight = 66731.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.066598 restraints weight = 32234.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.067999 restraints weight = 19744.695| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 24666 Z= 0.185 Angle : 0.647 18.899 33564 Z= 0.319 Chirality : 0.042 0.472 3606 Planarity : 0.005 0.052 4518 Dihedral : 3.910 16.079 3372 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.53 % Allowed : 14.74 % Favored : 82.73 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3090 helix: 0.71 (0.26), residues: 426 sheet: 0.28 (0.16), residues: 1050 loop : -0.78 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP J 23 HIS 0.003 0.001 HIS B 81 PHE 0.019 0.001 PHE Q 91 TYR 0.019 0.001 TYR R 198 ARG 0.003 0.000 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 840) hydrogen bonds : angle 5.23816 ( 2538) covalent geometry : bond 0.00425 (24660) covalent geometry : angle 0.64728 (33564) Misc. bond : bond 0.01527 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 455 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8305 (m) REVERT: A 55 ASN cc_start: 0.9274 (m-40) cc_final: 0.8933 (m-40) REVERT: A 112 LYS cc_start: 0.9179 (mmtt) cc_final: 0.8463 (mttt) REVERT: A 125 MET cc_start: 0.8788 (mmm) cc_final: 0.8510 (tpp) REVERT: B 78 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8295 (mtpp) REVERT: C 125 ILE cc_start: 0.9148 (mm) cc_final: 0.8928 (pt) REVERT: C 198 TYR cc_start: 0.9138 (m-80) cc_final: 0.8874 (m-80) REVERT: D 18 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8323 (m) REVERT: D 55 ASN cc_start: 0.9158 (m-40) cc_final: 0.8761 (m-40) REVERT: D 112 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8539 (mttt) REVERT: D 127 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8717 (ttmt) REVERT: E 57 ASP cc_start: 0.7865 (t0) cc_final: 0.7485 (t0) REVERT: E 78 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8365 (mtpp) REVERT: F 213 GLU cc_start: 0.8500 (tt0) cc_final: 0.8240 (tt0) REVERT: F 215 LYS cc_start: 0.9661 (tttt) cc_final: 0.9375 (tttm) REVERT: F 236 MET cc_start: 0.8574 (mmm) cc_final: 0.8256 (mmm) REVERT: F 238 MET cc_start: 0.8505 (tpp) cc_final: 0.8180 (tpp) REVERT: G 17 GLU cc_start: 0.9116 (pp20) cc_final: 0.8910 (pp20) REVERT: G 18 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.7833 (m) REVERT: G 79 GLU cc_start: 0.8180 (mp0) cc_final: 0.7568 (mp0) REVERT: G 112 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8562 (mttt) REVERT: H 78 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8304 (mtpp) REVERT: I 215 LYS cc_start: 0.9667 (tttt) cc_final: 0.9387 (tttm) REVERT: J 18 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8311 (m) REVERT: J 55 ASN cc_start: 0.9266 (m-40) cc_final: 0.8926 (m-40) REVERT: J 112 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8468 (mttt) REVERT: J 125 MET cc_start: 0.8790 (mmm) cc_final: 0.8531 (tpp) REVERT: K 14 GLU cc_start: 0.8232 (pm20) cc_final: 0.8004 (pm20) REVERT: K 78 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8294 (mtpp) REVERT: L 198 TYR cc_start: 0.9145 (m-80) cc_final: 0.8884 (m-80) REVERT: L 215 LYS cc_start: 0.9651 (tttt) cc_final: 0.9427 (tttm) REVERT: L 236 MET cc_start: 0.8762 (mmt) cc_final: 0.8114 (mmt) REVERT: M 18 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8319 (m) REVERT: M 55 ASN cc_start: 0.9141 (m-40) cc_final: 0.8746 (m-40) REVERT: M 112 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8528 (mttt) REVERT: M 127 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8709 (ttmt) REVERT: N 15 GLU cc_start: 0.8270 (mp0) cc_final: 0.7848 (mp0) REVERT: N 57 ASP cc_start: 0.7898 (t0) cc_final: 0.7653 (t0) REVERT: N 78 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8362 (mtpp) REVERT: O 213 GLU cc_start: 0.8498 (tt0) cc_final: 0.8235 (tt0) REVERT: O 215 LYS cc_start: 0.9659 (tttt) cc_final: 0.9377 (tttm) REVERT: O 236 MET cc_start: 0.8484 (mmm) cc_final: 0.8282 (mmm) REVERT: O 238 MET cc_start: 0.8509 (tpp) cc_final: 0.8212 (tpp) REVERT: P 18 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.7848 (m) REVERT: P 79 GLU cc_start: 0.8195 (mp0) cc_final: 0.7571 (mp0) REVERT: P 112 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8580 (mttt) REVERT: Q 15 GLU cc_start: 0.8076 (mp0) cc_final: 0.7827 (mp0) REVERT: Q 78 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8329 (mtpp) REVERT: R 215 LYS cc_start: 0.9670 (tttt) cc_final: 0.9390 (tttm) outliers start: 63 outliers final: 43 residues processed: 491 average time/residue: 0.3663 time to fit residues: 273.2498 Evaluate side-chains 488 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 439 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 110 MET Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 70 optimal weight: 0.0470 chunk 140 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 223 optimal weight: 0.0470 overall best weight: 2.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN I 209 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN O 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.075428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.064982 restraints weight = 66570.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.067082 restraints weight = 32502.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.068500 restraints weight = 19941.892| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 24666 Z= 0.157 Angle : 0.642 15.932 33564 Z= 0.314 Chirality : 0.041 0.442 3606 Planarity : 0.004 0.052 4518 Dihedral : 3.856 16.536 3372 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.65 % Allowed : 15.62 % Favored : 81.73 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 3090 helix: 0.54 (0.26), residues: 426 sheet: 0.27 (0.16), residues: 1050 loop : -0.74 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP J 23 HIS 0.003 0.001 HIS L 72 PHE 0.015 0.001 PHE H 91 TYR 0.018 0.001 TYR I 198 ARG 0.002 0.000 ARG F 27 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 840) hydrogen bonds : angle 5.16775 ( 2538) covalent geometry : bond 0.00367 (24660) covalent geometry : angle 0.64239 (33564) Misc. bond : bond 0.00738 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 454 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8201 (m) REVERT: A 55 ASN cc_start: 0.9294 (m-40) cc_final: 0.8972 (m-40) REVERT: A 99 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8439 (mtt90) REVERT: A 112 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8340 (mttt) REVERT: A 125 MET cc_start: 0.8771 (mmm) cc_final: 0.8492 (tpp) REVERT: B 78 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8336 (mtpp) REVERT: C 125 ILE cc_start: 0.9163 (mm) cc_final: 0.8941 (pt) REVERT: C 198 TYR cc_start: 0.9206 (m-80) cc_final: 0.8961 (m-80) REVERT: C 236 MET cc_start: 0.8689 (mmt) cc_final: 0.7926 (mmt) REVERT: D 18 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8328 (m) REVERT: D 55 ASN cc_start: 0.9177 (m-40) cc_final: 0.8781 (m-40) REVERT: D 112 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8514 (mttt) REVERT: D 127 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8784 (ttmt) REVERT: E 57 ASP cc_start: 0.7864 (t0) cc_final: 0.7448 (t0) REVERT: E 78 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8260 (mtpp) REVERT: F 215 LYS cc_start: 0.9646 (tttt) cc_final: 0.9343 (tttm) REVERT: F 236 MET cc_start: 0.8661 (mmm) cc_final: 0.8346 (mmm) REVERT: F 238 MET cc_start: 0.8560 (tpp) cc_final: 0.8188 (tpp) REVERT: G 18 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.7951 (m) REVERT: G 79 GLU cc_start: 0.8196 (mp0) cc_final: 0.7543 (mp0) REVERT: G 112 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8541 (mttt) REVERT: H 78 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8327 (mtpp) REVERT: I 215 LYS cc_start: 0.9665 (tttt) cc_final: 0.9378 (tttm) REVERT: J 18 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8218 (m) REVERT: J 55 ASN cc_start: 0.9290 (t0) cc_final: 0.8955 (m-40) REVERT: J 99 ARG cc_start: 0.8719 (mtp85) cc_final: 0.8432 (mtt90) REVERT: J 112 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8343 (mttt) REVERT: J 125 MET cc_start: 0.8770 (mmm) cc_final: 0.8473 (tpp) REVERT: K 78 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8340 (mtpp) REVERT: L 198 TYR cc_start: 0.9212 (m-80) cc_final: 0.8970 (m-80) REVERT: L 215 LYS cc_start: 0.9645 (tttt) cc_final: 0.9413 (tttm) REVERT: L 236 MET cc_start: 0.8790 (mmt) cc_final: 0.8045 (mmt) REVERT: M 18 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8328 (m) REVERT: M 55 ASN cc_start: 0.9175 (m-40) cc_final: 0.8782 (m-40) REVERT: M 112 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8489 (mttt) REVERT: M 127 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8782 (ttmt) REVERT: N 14 GLU cc_start: 0.7724 (pm20) cc_final: 0.7229 (pm20) REVERT: N 15 GLU cc_start: 0.8126 (mp0) cc_final: 0.7908 (mp0) REVERT: N 57 ASP cc_start: 0.7991 (t0) cc_final: 0.7666 (t0) REVERT: N 78 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8280 (mtpp) REVERT: O 215 LYS cc_start: 0.9648 (tttt) cc_final: 0.9348 (tttm) REVERT: O 236 MET cc_start: 0.8698 (mmm) cc_final: 0.8259 (mmm) REVERT: O 238 MET cc_start: 0.8503 (tpp) cc_final: 0.8162 (tpp) REVERT: P 17 GLU cc_start: 0.8954 (pp20) cc_final: 0.8700 (pp20) REVERT: P 18 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7705 (m) REVERT: P 79 GLU cc_start: 0.8201 (mp0) cc_final: 0.7959 (mt-10) REVERT: P 112 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8549 (mttt) REVERT: Q 78 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8309 (mtpp) REVERT: R 215 LYS cc_start: 0.9669 (tttt) cc_final: 0.9378 (tttm) outliers start: 66 outliers final: 43 residues processed: 493 average time/residue: 0.3696 time to fit residues: 277.3151 Evaluate side-chains 487 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 438 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 95 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN P 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.064456 restraints weight = 66837.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.066574 restraints weight = 32447.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.067966 restraints weight = 19755.592| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24666 Z= 0.188 Angle : 0.664 15.077 33564 Z= 0.323 Chirality : 0.040 0.143 3606 Planarity : 0.004 0.052 4518 Dihedral : 3.847 14.810 3372 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.45 % Allowed : 15.90 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3090 helix: 0.45 (0.26), residues: 426 sheet: 0.24 (0.16), residues: 1050 loop : -0.76 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 23 HIS 0.003 0.001 HIS N 120 PHE 0.015 0.001 PHE R 121 TYR 0.018 0.002 TYR R 198 ARG 0.002 0.000 ARG I 104 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 840) hydrogen bonds : angle 5.17360 ( 2538) covalent geometry : bond 0.00441 (24660) covalent geometry : angle 0.66369 (33564) Misc. bond : bond 0.00658 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 441 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 55 ASN cc_start: 0.9292 (m-40) cc_final: 0.8971 (m-40) REVERT: A 99 ARG cc_start: 0.8731 (mtp85) cc_final: 0.8461 (mtt90) REVERT: A 112 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8336 (mttt) REVERT: A 125 MET cc_start: 0.8770 (mmm) cc_final: 0.8492 (tpp) REVERT: B 14 GLU cc_start: 0.8210 (pm20) cc_final: 0.7984 (pm20) REVERT: B 78 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8312 (mtpp) REVERT: B 119 GLU cc_start: 0.7792 (mp0) cc_final: 0.7568 (mp0) REVERT: C 125 ILE cc_start: 0.9167 (mm) cc_final: 0.8951 (pt) REVERT: C 198 TYR cc_start: 0.9179 (m-80) cc_final: 0.8937 (m-80) REVERT: C 236 MET cc_start: 0.8755 (mmt) cc_final: 0.8031 (mmt) REVERT: D 18 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8342 (m) REVERT: D 55 ASN cc_start: 0.9179 (m-40) cc_final: 0.8772 (m-40) REVERT: D 112 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8494 (mttt) REVERT: D 127 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8736 (ttmt) REVERT: E 57 ASP cc_start: 0.7865 (t0) cc_final: 0.7488 (t0) REVERT: E 78 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8328 (mtpp) REVERT: F 215 LYS cc_start: 0.9647 (tttt) cc_final: 0.9342 (tttm) REVERT: F 236 MET cc_start: 0.8687 (mmm) cc_final: 0.8340 (mmm) REVERT: F 238 MET cc_start: 0.8536 (tpp) cc_final: 0.8172 (tpp) REVERT: G 18 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7584 (m) REVERT: G 79 GLU cc_start: 0.8225 (mp0) cc_final: 0.7590 (mp0) REVERT: G 112 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8545 (mttt) REVERT: H 78 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8331 (mtpp) REVERT: I 113 MET cc_start: 0.8394 (mmm) cc_final: 0.8157 (mmp) REVERT: I 215 LYS cc_start: 0.9667 (tttt) cc_final: 0.9380 (tttm) REVERT: J 18 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8214 (m) REVERT: J 55 ASN cc_start: 0.9287 (t0) cc_final: 0.8957 (m-40) REVERT: J 99 ARG cc_start: 0.8738 (mtp85) cc_final: 0.8454 (mtt90) REVERT: J 112 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8350 (mttt) REVERT: J 125 MET cc_start: 0.8763 (mmm) cc_final: 0.8490 (tpp) REVERT: K 37 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: K 78 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8354 (mtpp) REVERT: L 198 TYR cc_start: 0.9193 (m-80) cc_final: 0.8948 (m-80) REVERT: L 215 LYS cc_start: 0.9660 (tttt) cc_final: 0.9427 (tttm) REVERT: L 236 MET cc_start: 0.8758 (mmt) cc_final: 0.8034 (mmt) REVERT: M 18 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8347 (m) REVERT: M 55 ASN cc_start: 0.9176 (m-40) cc_final: 0.8774 (m-40) REVERT: M 112 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8497 (mttt) REVERT: M 127 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8735 (ttmt) REVERT: N 14 GLU cc_start: 0.7755 (pm20) cc_final: 0.7302 (pm20) REVERT: N 57 ASP cc_start: 0.8014 (t0) cc_final: 0.7722 (t0) REVERT: N 78 LYS cc_start: 0.8654 (mtpt) cc_final: 0.8334 (mtpp) REVERT: O 215 LYS cc_start: 0.9650 (tttt) cc_final: 0.9346 (tttm) REVERT: O 236 MET cc_start: 0.8556 (mmm) cc_final: 0.8267 (mmm) REVERT: O 238 MET cc_start: 0.8559 (tpp) cc_final: 0.8150 (tpp) REVERT: P 17 GLU cc_start: 0.9028 (pp20) cc_final: 0.8782 (pp20) REVERT: P 18 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7473 (m) REVERT: P 79 GLU cc_start: 0.8219 (mp0) cc_final: 0.7966 (mt-10) REVERT: P 112 LYS cc_start: 0.9171 (mmtt) cc_final: 0.8566 (mttt) REVERT: Q 14 GLU cc_start: 0.7977 (pm20) cc_final: 0.7696 (pm20) REVERT: Q 15 GLU cc_start: 0.7926 (mp0) cc_final: 0.7383 (mp0) REVERT: Q 78 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8349 (mtpp) REVERT: R 215 LYS cc_start: 0.9671 (tttt) cc_final: 0.9388 (tttm) outliers start: 61 outliers final: 46 residues processed: 478 average time/residue: 0.3977 time to fit residues: 291.2430 Evaluate side-chains 487 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 434 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 127 LYS Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 131 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 211 optimal weight: 0.0060 chunk 261 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 196 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 232 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 150 ASN O 86 ASN P 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.074293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.063965 restraints weight = 67053.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.066039 restraints weight = 32604.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.067433 restraints weight = 19911.503| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24666 Z= 0.210 Angle : 0.688 14.679 33564 Z= 0.340 Chirality : 0.041 0.246 3606 Planarity : 0.005 0.051 4518 Dihedral : 3.955 19.781 3372 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.45 % Allowed : 16.02 % Favored : 81.53 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3090 helix: 0.49 (0.26), residues: 426 sheet: 0.22 (0.16), residues: 1050 loop : -0.78 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 23 HIS 0.004 0.001 HIS N 120 PHE 0.016 0.002 PHE R 121 TYR 0.020 0.002 TYR R 198 ARG 0.003 0.000 ARG N 45 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 840) hydrogen bonds : angle 5.17979 ( 2538) covalent geometry : bond 0.00485 (24660) covalent geometry : angle 0.68817 (33564) Misc. bond : bond 0.00815 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 444 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.7759 (m) REVERT: A 55 ASN cc_start: 0.9297 (m-40) cc_final: 0.8960 (m-40) REVERT: A 99 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8464 (mtt90) REVERT: A 112 LYS cc_start: 0.9142 (mmtt) cc_final: 0.8349 (mttt) REVERT: A 125 MET cc_start: 0.8772 (mmm) cc_final: 0.8483 (tpp) REVERT: B 78 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8283 (mtpp) REVERT: B 119 GLU cc_start: 0.7856 (mp0) cc_final: 0.7609 (mp0) REVERT: C 125 ILE cc_start: 0.9263 (mm) cc_final: 0.8957 (pt) REVERT: C 198 TYR cc_start: 0.9196 (m-80) cc_final: 0.8962 (m-80) REVERT: C 236 MET cc_start: 0.8827 (mmt) cc_final: 0.8126 (mmt) REVERT: D 18 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8252 (m) REVERT: D 55 ASN cc_start: 0.9183 (m-40) cc_final: 0.8795 (m-40) REVERT: D 112 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8493 (mttt) REVERT: E 57 ASP cc_start: 0.7898 (t0) cc_final: 0.7537 (t0) REVERT: E 78 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8196 (mttp) REVERT: F 215 LYS cc_start: 0.9649 (tttt) cc_final: 0.9335 (tttm) REVERT: F 236 MET cc_start: 0.8705 (mmm) cc_final: 0.8336 (mmm) REVERT: F 238 MET cc_start: 0.8513 (tpp) cc_final: 0.8100 (tpp) REVERT: G 18 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7416 (m) REVERT: G 79 GLU cc_start: 0.8227 (mp0) cc_final: 0.7600 (mp0) REVERT: G 112 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8565 (mttt) REVERT: H 14 GLU cc_start: 0.8034 (pm20) cc_final: 0.7701 (pm20) REVERT: H 15 GLU cc_start: 0.8118 (mp0) cc_final: 0.7459 (mp0) REVERT: H 78 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8331 (mtpp) REVERT: I 113 MET cc_start: 0.8360 (mmm) cc_final: 0.8114 (mmp) REVERT: I 215 LYS cc_start: 0.9667 (tttt) cc_final: 0.9384 (tttm) REVERT: J 18 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.7759 (m) REVERT: J 55 ASN cc_start: 0.9294 (t0) cc_final: 0.8958 (m-40) REVERT: J 99 ARG cc_start: 0.8699 (mtp85) cc_final: 0.8408 (mtt90) REVERT: J 112 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8357 (mttt) REVERT: J 125 MET cc_start: 0.8771 (mmm) cc_final: 0.8484 (tpp) REVERT: K 37 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: K 78 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8285 (mtpp) REVERT: L 198 TYR cc_start: 0.9204 (m-80) cc_final: 0.8965 (m-80) REVERT: L 215 LYS cc_start: 0.9663 (tttt) cc_final: 0.9420 (tttm) REVERT: L 236 MET cc_start: 0.8774 (mmt) cc_final: 0.8061 (mmt) REVERT: M 18 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8280 (m) REVERT: M 55 ASN cc_start: 0.9177 (m-40) cc_final: 0.8768 (m-40) REVERT: M 112 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8506 (mttt) REVERT: N 34 ILE cc_start: 0.7880 (tp) cc_final: 0.7615 (tp) REVERT: N 57 ASP cc_start: 0.8059 (t0) cc_final: 0.7771 (t0) REVERT: N 78 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8194 (mtpp) REVERT: O 215 LYS cc_start: 0.9650 (tttt) cc_final: 0.9333 (tttm) REVERT: O 236 MET cc_start: 0.8734 (mmm) cc_final: 0.8348 (mmm) REVERT: O 238 MET cc_start: 0.8557 (tpp) cc_final: 0.8153 (tpp) REVERT: P 17 GLU cc_start: 0.9036 (pp20) cc_final: 0.8828 (pp20) REVERT: P 18 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7456 (m) REVERT: P 79 GLU cc_start: 0.8232 (mp0) cc_final: 0.7593 (mp0) REVERT: P 112 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8626 (mttt) REVERT: Q 14 GLU cc_start: 0.7978 (pm20) cc_final: 0.7645 (pm20) REVERT: Q 15 GLU cc_start: 0.7943 (mp0) cc_final: 0.7250 (mp0) REVERT: Q 78 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8389 (mtpp) REVERT: R 215 LYS cc_start: 0.9671 (tttt) cc_final: 0.9388 (tttm) outliers start: 61 outliers final: 48 residues processed: 479 average time/residue: 0.3995 time to fit residues: 291.6064 Evaluate side-chains 495 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 440 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 134 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 126 THR Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 37 GLU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 127 LYS Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 126 THR Chi-restraints excluded: chain R residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 129 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 0.0980 chunk 273 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 289 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN F 150 ASN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.064842 restraints weight = 66466.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.066964 restraints weight = 31731.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.068377 restraints weight = 19232.275| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24666 Z= 0.139 Angle : 0.681 16.673 33564 Z= 0.335 Chirality : 0.041 0.297 3606 Planarity : 0.004 0.051 4518 Dihedral : 3.835 14.978 3372 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.89 % Allowed : 16.75 % Favored : 81.37 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3090 helix: 0.68 (0.26), residues: 426 sheet: 0.25 (0.16), residues: 1050 loop : -0.70 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 23 HIS 0.004 0.001 HIS C 72 PHE 0.015 0.001 PHE H 91 TYR 0.018 0.001 TYR R 198 ARG 0.002 0.000 ARG F 219 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 840) hydrogen bonds : angle 5.07796 ( 2538) covalent geometry : bond 0.00316 (24660) covalent geometry : angle 0.68097 (33564) Misc. bond : bond 0.00829 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7130.24 seconds wall clock time: 125 minutes 42.12 seconds (7542.12 seconds total)