Starting phenix.real_space_refine on Fri Sep 19 06:53:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwa_63436/09_2025/9lwa_63436.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwa_63436/09_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_63436/09_2025/9lwa_63436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwa_63436/09_2025/9lwa_63436.map" model { file = "/net/cci-nas-00/data/ceres_data/9lwa_63436/09_2025/9lwa_63436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwa_63436/09_2025/9lwa_63436.cif" } resolution = 3.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: D, G, J, M, P, E, H, K, N, Q, F, I, L, O, R Time building chain proxies: 3.61, per 1000 atoms: 0.15 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: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.93 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: 4.67 Time building geometry restraints manager: 2.70 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' } 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' } 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.710 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (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 ARG 0.004 0.001 ARG B 89 TYR 0.012 0.001 TYR I 198 PHE 0.011 0.001 PHE K 88 TRP 0.004 0.001 TRP K 21 HIS 0.002 0.001 HIS G 40 Details of bonding type rmsd covalent geometry : bond 0.00274 (24660) covalent geometry : angle 0.57294 (33564) hydrogen bonds : bond 0.25869 ( 840) hydrogen bonds : angle 8.92969 ( 2538) 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 : 0.863 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: 0.8341 (mttt) REVERT: B 15 GLU cc_start: 0.8151 (mp0) cc_final: 0.7722 (mp0) REVERT: B 40 PHE cc_start: 0.8295 (t80) cc_final: 0.7430 (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: 0.8907 (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: 0.7736 (tm-30) REVERT: C 236 MET cc_start: 0.8056 (mmt) cc_final: 0.7020 (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: 0.8370 (mttt) REVERT: D 113 TYR cc_start: 0.8775 (m-80) cc_final: 0.8501 (m-80) REVERT: E 78 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8180 (mtpp) REVERT: E 89 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8406 (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: 0.7726 (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: 0.8342 (mttt) REVERT: H 14 GLU cc_start: 0.7677 (pm20) cc_final: 0.7462 (pm20) REVERT: H 15 GLU cc_start: 0.7875 (mp0) cc_final: 0.7039 (mp0) REVERT: H 78 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8171 (mtpp) REVERT: H 127 THR cc_start: 0.9473 (m) cc_final: 0.9164 (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: 0.8109 (m-80) REVERT: I 114 ILE cc_start: 0.8544 (mm) cc_final: 0.8297 (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: 0.8898 (tt) REVERT: J 112 LYS cc_start: 0.9149 (mmtt) cc_final: 0.8309 (mttt) REVERT: K 40 PHE cc_start: 0.8279 (t80) cc_final: 0.7395 (t80) REVERT: K 78 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8277 (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: 0.7439 (mmp) REVERT: M 4 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7894 (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: 0.8509 (m-80) REVERT: N 78 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8191 (mtpp) REVERT: N 89 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8443 (mmm160) REVERT: N 127 THR cc_start: 0.9424 (m) cc_final: 0.9031 (p) REVERT: O 125 ILE cc_start: 0.8834 (mm) cc_final: 0.8369 (mm) REVERT: O 199 GLU cc_start: 0.7947 (tt0) cc_final: 0.7719 (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: 0.8179 (mmm) REVERT: P 112 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8307 (mttt) REVERT: P 113 TYR cc_start: 0.8837 (m-80) cc_final: 0.8625 (m-80) REVERT: Q 15 GLU cc_start: 0.7861 (mp0) cc_final: 0.7037 (mp0) REVERT: Q 78 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8172 (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: 0.8279 (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: 0.8509 (pttm) outliers start: 0 outliers final: 0 residues processed: 674 average time/residue: 0.1893 time to fit residues: 192.9820 Evaluate side-chains 511 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 GLN I 150 ASN I 209 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 ASN O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 ASN R 86 ASN R 138 GLN R 150 ASN R 209 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.073244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.062799 restraints weight = 68199.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.064863 restraints weight = 33112.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.066273 restraints weight = 20298.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.067221 restraints weight = 14226.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.067865 restraints weight = 10945.673| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 24666 Z= 0.395 Angle : 0.753 9.416 33564 Z= 0.384 Chirality : 0.045 0.199 3606 Planarity : 0.006 0.043 4518 Dihedral : 4.410 18.843 3372 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.29 % Allowed : 10.44 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.14), residues: 3090 helix: 0.27 (0.25), residues: 426 sheet: 0.15 (0.16), residues: 1002 loop : -0.98 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 104 TYR 0.014 0.002 TYR G 113 PHE 0.026 0.003 PHE O 121 TRP 0.010 0.002 TRP I 89 HIS 0.007 0.002 HIS J 40 Details of bonding type rmsd covalent geometry : bond 0.00897 (24660) covalent geometry : angle 0.75270 (33564) hydrogen bonds : bond 0.05355 ( 840) hydrogen bonds : angle 6.18246 ( 2538) Misc. bond : bond 0.00194 ( 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 508 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 451 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.9191 (m-40) cc_final: 0.8820 (m-40) REVERT: A 99 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8432 (mtt90) REVERT: A 112 LYS cc_start: 0.9230 (mmtt) cc_final: 0.8440 (mttt) REVERT: A 125 MET cc_start: 0.8886 (mmm) cc_final: 0.8522 (tpp) REVERT: B 15 GLU cc_start: 0.8024 (mp0) cc_final: 0.7735 (mp0) REVERT: B 37 GLU cc_start: 0.8241 (pm20) cc_final: 0.7931 (pm20) REVERT: B 40 PHE cc_start: 0.8441 (t80) cc_final: 0.7984 (t80) REVERT: B 78 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8341 (mtpp) REVERT: C 125 ILE cc_start: 0.9136 (mm) cc_final: 0.8929 (pt) REVERT: C 215 LYS cc_start: 0.9631 (tttt) cc_final: 0.9403 (tttm) REVERT: D 55 ASN cc_start: 0.9178 (m-40) cc_final: 0.8848 (m-40) REVERT: D 112 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8577 (mtpt) REVERT: E 15 GLU cc_start: 0.8254 (mp0) cc_final: 0.7919 (mp0) REVERT: E 78 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8309 (mtpp) REVERT: E 127 THR cc_start: 0.9300 (m) cc_final: 0.8935 (p) REVERT: F 213 GLU cc_start: 0.8491 (tt0) cc_final: 0.8287 (tt0) REVERT: F 236 MET cc_start: 0.8523 (mmm) cc_final: 0.7917 (mmm) REVERT: G 79 GLU cc_start: 0.8266 (mp0) cc_final: 0.7721 (mp0) REVERT: G 112 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8576 (mtpt) REVERT: H 14 GLU cc_start: 0.7888 (pm20) cc_final: 0.7520 (pm20) REVERT: H 15 GLU cc_start: 0.7915 (mp0) cc_final: 0.7299 (mp0) REVERT: H 46 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8744 (mt) REVERT: H 78 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8209 (mtpp) REVERT: H 127 THR cc_start: 0.9355 (m) cc_final: 0.9092 (p) REVERT: J 55 ASN cc_start: 0.9182 (m-40) cc_final: 0.8814 (m-40) REVERT: J 99 ARG cc_start: 0.8745 (mtp85) cc_final: 0.8430 (mtt90) REVERT: J 112 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8437 (mttt) REVERT: J 125 MET cc_start: 0.8880 (mmm) cc_final: 0.8541 (tpp) REVERT: K 37 GLU cc_start: 0.8246 (pm20) cc_final: 0.7932 (pm20) REVERT: K 40 PHE cc_start: 0.8453 (t80) cc_final: 0.8001 (t80) REVERT: K 78 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8364 (mtpp) REVERT: L 125 ILE cc_start: 0.9169 (mm) cc_final: 0.8831 (pt) REVERT: L 215 LYS cc_start: 0.9634 (tttt) cc_final: 0.9409 (tttm) REVERT: M 55 ASN cc_start: 0.9175 (m-40) cc_final: 0.8853 (m-40) REVERT: M 112 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8539 (mttt) REVERT: M 127 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8625 (ttpt) REVERT: N 15 GLU cc_start: 0.8178 (mp0) cc_final: 0.7782 (mp0) REVERT: N 78 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8274 (mtpp) REVERT: N 127 THR cc_start: 0.9298 (m) cc_final: 0.8929 (p) REVERT: O 178 GLU cc_start: 0.7499 (pm20) cc_final: 0.7168 (mp0) REVERT: O 236 MET cc_start: 0.8692 (mmt) cc_final: 0.8082 (mmm) REVERT: P 79 GLU cc_start: 0.8283 (mp0) cc_final: 0.7720 (mp0) REVERT: P 112 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8540 (mttt) REVERT: Q 14 GLU cc_start: 0.7655 (pm20) cc_final: 0.7062 (pm20) REVERT: Q 15 GLU cc_start: 0.7691 (mp0) cc_final: 0.7421 (mp0) REVERT: Q 78 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8215 (mtpp) REVERT: Q 127 THR cc_start: 0.9350 (m) cc_final: 0.9107 (p) outliers start: 57 outliers final: 34 residues processed: 477 average time/residue: 0.1810 time to fit residues: 129.1582 Evaluate side-chains 451 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 416 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain B residue 28 THR 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 D residue 94 ASP Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 162 VAL 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 28 THR Chi-restraints excluded: chain L residue 126 THR Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 162 VAL 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 74 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN I 150 ASN L 86 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.074716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.064207 restraints weight = 67130.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.066351 restraints weight = 32169.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.067797 restraints weight = 19490.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.068739 restraints weight = 13537.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.069430 restraints weight = 10345.583| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24666 Z= 0.176 Angle : 0.594 10.387 33564 Z= 0.298 Chirality : 0.041 0.155 3606 Planarity : 0.005 0.050 4518 Dihedral : 4.108 17.579 3372 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.05 % Allowed : 12.81 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.15), residues: 3090 helix: 0.68 (0.25), residues: 426 sheet: 0.36 (0.16), residues: 1032 loop : -0.93 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 27 TYR 0.019 0.001 TYR P 113 PHE 0.014 0.001 PHE F 121 TRP 0.016 0.002 TRP A 23 HIS 0.004 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00405 (24660) covalent geometry : angle 0.59450 (33564) hydrogen bonds : bond 0.04137 ( 840) hydrogen bonds : angle 5.67942 ( 2538) Misc. bond : bond 0.00351 ( 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 530 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 479 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.9260 (m-40) cc_final: 0.8940 (m-40) REVERT: A 99 ARG cc_start: 0.8703 (mtp85) cc_final: 0.8403 (mtt90) REVERT: A 112 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8438 (mtpt) REVERT: A 125 MET cc_start: 0.8832 (mmm) cc_final: 0.8399 (tpp) REVERT: B 40 PHE cc_start: 0.8431 (t80) cc_final: 0.7778 (t80) REVERT: B 57 ASP cc_start: 0.8162 (m-30) cc_final: 0.7741 (t0) REVERT: B 78 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8324 (mtpp) REVERT: C 198 TYR cc_start: 0.9230 (m-80) cc_final: 0.8830 (m-80) REVERT: C 215 LYS cc_start: 0.9600 (tttt) cc_final: 0.9319 (tttm) REVERT: D 55 ASN cc_start: 0.9195 (m-40) cc_final: 0.8826 (m-40) REVERT: D 112 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8558 (mttt) REVERT: E 14 GLU cc_start: 0.7994 (pm20) cc_final: 0.7606 (pm20) REVERT: E 15 GLU cc_start: 0.8107 (mp0) cc_final: 0.7651 (mp0) REVERT: E 31 GLU cc_start: 0.8176 (tp30) cc_final: 0.7965 (tp30) REVERT: E 78 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8250 (mtpp) REVERT: F 213 GLU cc_start: 0.8487 (tt0) cc_final: 0.8236 (tt0) REVERT: F 236 MET cc_start: 0.8474 (mmm) cc_final: 0.8055 (mmm) REVERT: G 79 GLU cc_start: 0.8170 (mp0) cc_final: 0.7536 (mp0) REVERT: G 112 LYS cc_start: 0.9157 (mmtt) cc_final: 0.8471 (mttt) REVERT: H 14 GLU cc_start: 0.7914 (pm20) cc_final: 0.7653 (pm20) REVERT: H 15 GLU cc_start: 0.7733 (mp0) cc_final: 0.7486 (mp0) REVERT: H 78 LYS cc_start: 0.8694 (mtpt) cc_final: 0.8211 (mtpp) REVERT: H 136 TYR cc_start: 0.8412 (m-80) cc_final: 0.8107 (m-80) REVERT: I 213 GLU cc_start: 0.8326 (tt0) cc_final: 0.8087 (tt0) REVERT: I 215 LYS cc_start: 0.9619 (tttt) cc_final: 0.9341 (tttm) REVERT: J 55 ASN cc_start: 0.9248 (m-40) cc_final: 0.8926 (m-40) REVERT: J 99 ARG cc_start: 0.8705 (mtp85) cc_final: 0.8406 (mtt90) REVERT: J 112 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8425 (mtpt) REVERT: J 125 MET cc_start: 0.8832 (mmm) cc_final: 0.8419 (tpp) REVERT: K 31 GLU cc_start: 0.8252 (tp30) cc_final: 0.7836 (tp30) REVERT: K 40 PHE cc_start: 0.8439 (t80) cc_final: 0.7837 (t80) REVERT: K 78 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8292 (mtpp) REVERT: L 125 ILE cc_start: 0.9151 (mm) cc_final: 0.8910 (mm) REVERT: L 198 TYR cc_start: 0.9189 (m-80) cc_final: 0.8769 (m-80) REVERT: L 215 LYS cc_start: 0.9602 (tttt) cc_final: 0.9325 (tttm) REVERT: M 55 ASN cc_start: 0.9173 (m-40) cc_final: 0.8809 (m-40) REVERT: M 112 LYS cc_start: 0.9110 (mmtt) cc_final: 0.8551 (mttt) REVERT: M 127 LYS cc_start: 0.8940 (ttmm) cc_final: 0.8580 (ttmt) REVERT: N 14 GLU cc_start: 0.7966 (pm20) cc_final: 0.7525 (pm20) REVERT: N 15 GLU cc_start: 0.8230 (mp0) cc_final: 0.7806 (mp0) REVERT: N 31 GLU cc_start: 0.8183 (tp30) cc_final: 0.7956 (tp30) REVERT: N 37 GLU cc_start: 0.8197 (pm20) cc_final: 0.7889 (pm20) REVERT: N 57 ASP cc_start: 0.8193 (t0) cc_final: 0.7965 (t0) REVERT: N 78 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8241 (mtpp) REVERT: O 178 GLU cc_start: 0.7442 (pm20) cc_final: 0.7096 (mp0) REVERT: O 213 GLU cc_start: 0.8521 (tt0) cc_final: 0.8279 (tt0) REVERT: O 236 MET cc_start: 0.8749 (mmt) cc_final: 0.8031 (mmm) REVERT: P 79 GLU cc_start: 0.8187 (mp0) cc_final: 0.7307 (mp0) REVERT: P 112 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8564 (mttt) REVERT: Q 78 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8210 (mtpp) REVERT: R 213 GLU cc_start: 0.8327 (tt0) cc_final: 0.8084 (tt0) REVERT: R 215 LYS cc_start: 0.9619 (tttt) cc_final: 0.9345 (tttm) outliers start: 51 outliers final: 32 residues processed: 510 average time/residue: 0.1839 time to fit residues: 141.9072 Evaluate side-chains 478 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 446 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 SER Chi-restraints excluded: chain D residue 127 LYS 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 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 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 45 SER Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR 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 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 63 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 6 optimal weight: 0.0970 chunk 108 optimal weight: 7.9990 chunk 95 optimal weight: 0.4980 chunk 114 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 4.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.073898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.063326 restraints weight = 67176.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.065396 restraints weight = 33005.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.066796 restraints weight = 20345.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.067733 restraints weight = 14348.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.068375 restraints weight = 11104.843| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24666 Z= 0.216 Angle : 0.609 9.421 33564 Z= 0.306 Chirality : 0.041 0.153 3606 Planarity : 0.005 0.052 4518 Dihedral : 4.103 17.845 3372 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.69 % Allowed : 14.26 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 3090 helix: 0.74 (0.26), residues: 426 sheet: 0.35 (0.16), residues: 1032 loop : -1.00 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 27 TYR 0.018 0.002 TYR G 113 PHE 0.017 0.002 PHE F 121 TRP 0.009 0.002 TRP P 23 HIS 0.004 0.001 HIS K 81 Details of bonding type rmsd covalent geometry : bond 0.00495 (24660) covalent geometry : angle 0.60853 (33564) hydrogen bonds : bond 0.04063 ( 840) hydrogen bonds : angle 5.50930 ( 2538) Misc. bond : bond 0.00643 ( 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 527 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 460 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8572 (m) REVERT: A 55 ASN cc_start: 0.9243 (m-40) cc_final: 0.8919 (m-40) REVERT: A 99 ARG cc_start: 0.8719 (mtp85) cc_final: 0.8439 (mtt90) REVERT: A 112 LYS cc_start: 0.9182 (mmtt) cc_final: 0.8456 (mtpt) REVERT: A 125 MET cc_start: 0.8813 (mmm) cc_final: 0.8552 (tpp) REVERT: B 15 GLU cc_start: 0.8237 (mp0) cc_final: 0.8024 (mp0) REVERT: B 40 PHE cc_start: 0.8414 (t80) cc_final: 0.7886 (t80) REVERT: B 78 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8320 (mtpp) REVERT: C 125 ILE cc_start: 0.9159 (mm) cc_final: 0.8844 (pt) REVERT: C 198 TYR cc_start: 0.9181 (m-80) cc_final: 0.8831 (m-80) REVERT: C 215 LYS cc_start: 0.9621 (tttt) cc_final: 0.9366 (tttm) REVERT: C 236 MET cc_start: 0.8727 (mmt) cc_final: 0.7916 (mmp) REVERT: D 55 ASN cc_start: 0.9201 (m-40) cc_final: 0.8858 (m-40) REVERT: D 112 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8568 (mttt) REVERT: E 14 GLU cc_start: 0.7973 (pm20) cc_final: 0.7715 (pm20) REVERT: E 15 GLU cc_start: 0.8164 (mp0) cc_final: 0.7582 (mp0) REVERT: E 78 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8241 (mtpp) REVERT: E 119 GLU cc_start: 0.7601 (mp0) cc_final: 0.7376 (mp0) REVERT: F 213 GLU cc_start: 0.8493 (tt0) cc_final: 0.8205 (tt0) REVERT: F 236 MET cc_start: 0.8504 (mmm) cc_final: 0.8232 (mmm) REVERT: F 238 MET cc_start: 0.8393 (tpp) cc_final: 0.8126 (tpp) REVERT: G 18 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8224 (m) REVERT: G 79 GLU cc_start: 0.8235 (mp0) cc_final: 0.7411 (mp0) REVERT: G 112 LYS cc_start: 0.9169 (mmtt) cc_final: 0.8526 (mttt) REVERT: H 15 GLU cc_start: 0.7706 (mp0) cc_final: 0.7381 (mp0) REVERT: H 31 GLU cc_start: 0.7762 (tp30) cc_final: 0.7450 (tp30) REVERT: H 47 ASP cc_start: 0.8074 (m-30) cc_final: 0.7832 (m-30) REVERT: H 78 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8174 (mtpp) REVERT: I 213 GLU cc_start: 0.8302 (tt0) cc_final: 0.8022 (tt0) REVERT: I 215 LYS cc_start: 0.9644 (tttt) cc_final: 0.9335 (tttm) REVERT: J 18 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8538 (m) REVERT: J 55 ASN cc_start: 0.9252 (m-40) cc_final: 0.8964 (m-40) REVERT: J 112 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8447 (mtpt) REVERT: J 125 MET cc_start: 0.8830 (mmm) cc_final: 0.8542 (tpp) REVERT: K 40 PHE cc_start: 0.8496 (t80) cc_final: 0.7967 (t80) REVERT: K 78 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8277 (mtpp) REVERT: L 125 ILE cc_start: 0.9153 (mm) cc_final: 0.8774 (pt) REVERT: L 198 TYR cc_start: 0.9181 (m-80) cc_final: 0.8628 (m-80) REVERT: L 215 LYS cc_start: 0.9622 (tttt) cc_final: 0.9370 (tttm) REVERT: L 236 MET cc_start: 0.8689 (mmt) cc_final: 0.7916 (mmt) REVERT: M 55 ASN cc_start: 0.9189 (m-40) cc_final: 0.8855 (m-40) REVERT: M 112 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8571 (mttt) REVERT: M 127 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8566 (ttmt) REVERT: N 14 GLU cc_start: 0.7961 (pm20) cc_final: 0.7706 (pm20) REVERT: N 15 GLU cc_start: 0.8271 (mp0) cc_final: 0.7794 (mp0) REVERT: N 37 GLU cc_start: 0.8210 (pm20) cc_final: 0.8001 (pm20) REVERT: N 57 ASP cc_start: 0.8204 (t0) cc_final: 0.7917 (t0) REVERT: N 78 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8241 (mtpp) REVERT: O 178 GLU cc_start: 0.7306 (pm20) cc_final: 0.7041 (mp0) REVERT: O 213 GLU cc_start: 0.8525 (tt0) cc_final: 0.8315 (tt0) REVERT: O 236 MET cc_start: 0.8800 (mmt) cc_final: 0.8175 (mmm) REVERT: O 238 MET cc_start: 0.8466 (tpp) cc_final: 0.8212 (tpp) REVERT: P 18 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8234 (m) REVERT: P 79 GLU cc_start: 0.8243 (mp0) cc_final: 0.7411 (mp0) REVERT: P 112 LYS cc_start: 0.9196 (mmtt) cc_final: 0.8556 (mttt) REVERT: Q 15 GLU cc_start: 0.7635 (mp0) cc_final: 0.7391 (mp0) REVERT: Q 31 GLU cc_start: 0.7799 (tp30) cc_final: 0.7479 (tp30) REVERT: Q 78 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8172 (mtpp) REVERT: R 215 LYS cc_start: 0.9647 (tttt) cc_final: 0.9326 (tttm) outliers start: 67 outliers final: 49 residues processed: 490 average time/residue: 0.1769 time to fit residues: 132.2710 Evaluate side-chains 497 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 444 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 B residue 26 MET 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 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 127 LYS 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 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 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 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 134 THR Chi-restraints excluded: chain L residue 33 VAL 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 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 Q residue 38 LEU Chi-restraints excluded: chain Q residue 56 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 5 optimal weight: 0.8980 chunk 259 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.064687 restraints weight = 66367.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.066798 restraints weight = 32477.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.068222 restraints weight = 20019.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.069180 restraints weight = 14055.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.069831 restraints weight = 10815.597| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24666 Z= 0.138 Angle : 0.577 9.960 33564 Z= 0.287 Chirality : 0.040 0.136 3606 Planarity : 0.004 0.052 4518 Dihedral : 3.935 16.329 3372 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.61 % Allowed : 15.38 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 3090 helix: 0.96 (0.26), residues: 426 sheet: 0.39 (0.16), residues: 1044 loop : -0.94 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 27 TYR 0.018 0.001 TYR G 113 PHE 0.010 0.001 PHE F 121 TRP 0.015 0.001 TRP G 23 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00320 (24660) covalent geometry : angle 0.57732 (33564) hydrogen bonds : bond 0.03630 ( 840) hydrogen bonds : angle 5.32176 ( 2538) Misc. bond : bond 0.00650 ( 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 535 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 470 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASN cc_start: 0.9263 (m-40) cc_final: 0.8952 (m-40) REVERT: A 112 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8421 (mttt) REVERT: A 125 MET cc_start: 0.8799 (mmm) cc_final: 0.8510 (tpp) REVERT: B 31 GLU cc_start: 0.8264 (tp30) cc_final: 0.7934 (tp30) REVERT: B 78 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8275 (mtpp) REVERT: C 198 TYR cc_start: 0.9201 (m-80) cc_final: 0.8999 (m-80) REVERT: C 215 LYS cc_start: 0.9609 (tttt) cc_final: 0.9356 (tttm) REVERT: C 236 MET cc_start: 0.8712 (mmt) cc_final: 0.7714 (mmm) REVERT: D 18 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8426 (m) REVERT: D 55 ASN cc_start: 0.9192 (m-40) cc_final: 0.8825 (m-40) REVERT: D 112 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8513 (mttt) REVERT: D 127 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8772 (ttmt) REVERT: E 31 GLU cc_start: 0.7757 (tp30) cc_final: 0.7554 (tp30) REVERT: E 37 GLU cc_start: 0.8183 (pm20) cc_final: 0.7933 (mp0) REVERT: E 78 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8220 (mtpp) REVERT: F 213 GLU cc_start: 0.8496 (tt0) cc_final: 0.8212 (tt0) REVERT: F 236 MET cc_start: 0.8625 (mmm) cc_final: 0.8238 (mmm) REVERT: G 17 GLU cc_start: 0.9046 (pp20) cc_final: 0.8799 (pp20) REVERT: G 18 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.7938 (m) REVERT: G 79 GLU cc_start: 0.8224 (mp0) cc_final: 0.7937 (mt-10) REVERT: G 112 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8535 (mttt) REVERT: H 31 GLU cc_start: 0.7593 (tp30) cc_final: 0.7392 (tp30) REVERT: H 78 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8179 (mtpp) REVERT: H 136 TYR cc_start: 0.8349 (m-80) cc_final: 0.7956 (m-80) REVERT: I 213 GLU cc_start: 0.8329 (tt0) cc_final: 0.8118 (tt0) REVERT: I 215 LYS cc_start: 0.9645 (tttt) cc_final: 0.9397 (tttm) REVERT: I 236 MET cc_start: 0.8734 (mmm) cc_final: 0.8523 (mmp) REVERT: J 55 ASN cc_start: 0.9254 (m-40) cc_final: 0.8946 (m-40) REVERT: J 99 ARG cc_start: 0.8692 (mtp85) cc_final: 0.8418 (mtt90) REVERT: J 112 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8421 (mttt) REVERT: J 125 MET cc_start: 0.8800 (mmm) cc_final: 0.8514 (tpp) REVERT: K 31 GLU cc_start: 0.7955 (tp30) cc_final: 0.7600 (tp30) REVERT: K 78 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8306 (mtpp) REVERT: L 124 ASP cc_start: 0.8588 (t0) cc_final: 0.8387 (t0) REVERT: L 125 ILE cc_start: 0.9111 (mm) cc_final: 0.8887 (mm) REVERT: L 198 TYR cc_start: 0.9202 (m-80) cc_final: 0.8998 (m-80) REVERT: L 215 LYS cc_start: 0.9612 (tttt) cc_final: 0.9359 (tttm) REVERT: L 236 MET cc_start: 0.8718 (mmt) cc_final: 0.7721 (mmm) REVERT: M 18 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8423 (m) REVERT: M 55 ASN cc_start: 0.9181 (m-40) cc_final: 0.8830 (m-40) REVERT: M 112 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8513 (mttt) REVERT: M 127 LYS cc_start: 0.8938 (ttmm) cc_final: 0.8636 (ttmt) REVERT: N 37 GLU cc_start: 0.8175 (pm20) cc_final: 0.7938 (mp0) REVERT: N 57 ASP cc_start: 0.8050 (t0) cc_final: 0.7740 (t0) REVERT: N 78 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8225 (mtpp) REVERT: N 119 GLU cc_start: 0.7857 (mp0) cc_final: 0.7564 (mp0) REVERT: O 178 GLU cc_start: 0.7172 (pm20) cc_final: 0.6925 (mp0) REVERT: O 236 MET cc_start: 0.8832 (mmt) cc_final: 0.8159 (mmm) REVERT: O 238 MET cc_start: 0.8379 (tpp) cc_final: 0.8083 (tpp) REVERT: P 18 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.7949 (m) REVERT: P 79 GLU cc_start: 0.8221 (mp0) cc_final: 0.7965 (mt-10) REVERT: P 112 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8491 (mttt) REVERT: Q 31 GLU cc_start: 0.7618 (tp30) cc_final: 0.7416 (tp30) REVERT: Q 78 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8173 (mtpp) REVERT: Q 136 TYR cc_start: 0.8338 (m-80) cc_final: 0.7938 (m-80) REVERT: R 213 GLU cc_start: 0.8329 (tt0) cc_final: 0.8115 (tt0) REVERT: R 215 LYS cc_start: 0.9648 (tttt) cc_final: 0.9346 (tttm) outliers start: 65 outliers final: 39 residues processed: 502 average time/residue: 0.1794 time to fit residues: 137.5400 Evaluate side-chains 489 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 446 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 44 THR 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 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 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 110 MET Chi-restraints excluded: chain H residue 37 GLU 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 63 LEU Chi-restraints excluded: chain J residue 126 CYS 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 243 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 142 optimal weight: 0.0020 chunk 181 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.073567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.063058 restraints weight = 67243.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.065135 restraints weight = 32842.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.066543 restraints weight = 20147.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.067462 restraints weight = 14128.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.068137 restraints weight = 10922.419| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 24666 Z= 0.237 Angle : 0.654 11.485 33564 Z= 0.323 Chirality : 0.041 0.157 3606 Planarity : 0.005 0.052 4518 Dihedral : 4.087 17.654 3372 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.45 % Allowed : 14.94 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 3090 helix: 0.79 (0.26), residues: 426 sheet: 0.31 (0.16), residues: 1044 loop : -1.00 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 104 TYR 0.019 0.002 TYR I 198 PHE 0.018 0.002 PHE O 121 TRP 0.014 0.002 TRP M 23 HIS 0.004 0.001 HIS N 120 Details of bonding type rmsd covalent geometry : bond 0.00543 (24660) covalent geometry : angle 0.65416 (33564) hydrogen bonds : bond 0.04050 ( 840) hydrogen bonds : angle 5.30312 ( 2538) Misc. bond : bond 0.00648 ( 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 525 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 439 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8460 (m) REVERT: A 55 ASN cc_start: 0.9286 (m-40) cc_final: 0.8936 (m-40) REVERT: A 99 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8477 (mtt90) REVERT: A 112 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8435 (mttt) REVERT: A 125 MET cc_start: 0.8786 (mmm) cc_final: 0.8495 (tpp) REVERT: B 78 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8309 (mtpp) REVERT: C 125 ILE cc_start: 0.9243 (mm) cc_final: 0.8860 (pt) REVERT: C 198 TYR cc_start: 0.9234 (m-80) cc_final: 0.9034 (m-80) REVERT: C 215 LYS cc_start: 0.9652 (tttt) cc_final: 0.9402 (tttm) REVERT: C 236 MET cc_start: 0.8820 (mmt) cc_final: 0.7878 (mmm) REVERT: D 18 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8358 (m) REVERT: D 55 ASN cc_start: 0.9213 (m-40) cc_final: 0.8867 (m-40) REVERT: D 112 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8526 (mttt) REVERT: E 15 GLU cc_start: 0.7939 (mp0) cc_final: 0.7542 (mp0) REVERT: E 37 GLU cc_start: 0.8278 (pm20) cc_final: 0.7992 (mp0) REVERT: E 78 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8273 (mtpp) REVERT: E 119 GLU cc_start: 0.7984 (mp0) cc_final: 0.7750 (mp0) REVERT: F 213 GLU cc_start: 0.8516 (tt0) cc_final: 0.8200 (tt0) REVERT: F 236 MET cc_start: 0.8648 (mmm) cc_final: 0.8302 (mmm) REVERT: G 18 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.7738 (m) REVERT: G 79 GLU cc_start: 0.8231 (mp0) cc_final: 0.7587 (mp0) REVERT: G 112 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8583 (mttt) REVERT: H 15 GLU cc_start: 0.8017 (mp0) cc_final: 0.7809 (mp0) REVERT: H 78 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8278 (mtpp) REVERT: H 136 TYR cc_start: 0.8395 (m-80) cc_final: 0.8082 (m-80) REVERT: I 113 MET cc_start: 0.8399 (mmm) cc_final: 0.8136 (mmp) REVERT: I 215 LYS cc_start: 0.9655 (tttt) cc_final: 0.9353 (tttm) REVERT: J 18 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8432 (m) REVERT: J 55 ASN cc_start: 0.9287 (m-40) cc_final: 0.8973 (m-40) REVERT: J 99 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8473 (mtt90) REVERT: J 112 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8430 (mttt) REVERT: J 125 MET cc_start: 0.8778 (mmm) cc_final: 0.8474 (tpp) REVERT: K 31 GLU cc_start: 0.7923 (tp30) cc_final: 0.7682 (tp30) REVERT: K 78 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8311 (mtpp) REVERT: L 125 ILE cc_start: 0.9233 (mm) cc_final: 0.8780 (pt) REVERT: L 215 LYS cc_start: 0.9654 (tttt) cc_final: 0.9406 (tttm) REVERT: L 236 MET cc_start: 0.8824 (mmt) cc_final: 0.7879 (mmm) REVERT: M 18 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8343 (m) REVERT: M 55 ASN cc_start: 0.9194 (m-40) cc_final: 0.8845 (m-40) REVERT: M 112 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8499 (mttt) REVERT: M 127 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8565 (ttmt) REVERT: N 15 GLU cc_start: 0.7944 (mp0) cc_final: 0.7581 (mp0) REVERT: N 37 GLU cc_start: 0.8262 (pm20) cc_final: 0.7993 (mp0) REVERT: N 57 ASP cc_start: 0.8031 (t0) cc_final: 0.7738 (m-30) REVERT: N 78 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8282 (mtpp) REVERT: N 119 GLU cc_start: 0.8000 (mp0) cc_final: 0.7716 (mp0) REVERT: O 213 GLU cc_start: 0.8577 (tt0) cc_final: 0.8308 (tt0) REVERT: O 236 MET cc_start: 0.8847 (mmt) cc_final: 0.8156 (mmm) REVERT: O 238 MET cc_start: 0.8456 (tpp) cc_final: 0.8193 (tpp) REVERT: P 18 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7768 (m) REVERT: P 79 GLU cc_start: 0.8216 (mp0) cc_final: 0.7546 (mp0) REVERT: P 112 LYS cc_start: 0.9155 (mmtt) cc_final: 0.8562 (mttt) REVERT: Q 78 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8268 (mtpp) REVERT: Q 136 TYR cc_start: 0.8372 (m-80) cc_final: 0.8041 (m-80) REVERT: R 113 MET cc_start: 0.8397 (mmm) cc_final: 0.8143 (mmp) REVERT: R 215 LYS cc_start: 0.9656 (tttt) cc_final: 0.9350 (tttm) outliers start: 86 outliers final: 55 residues processed: 483 average time/residue: 0.1747 time to fit residues: 128.8426 Evaluate side-chains 491 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 430 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 37 GLU 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 107 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 72 LEU 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 45 SER 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 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 63 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 26 MET Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 31 ILE 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 M residue 18 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 72 LEU 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 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 45 SER 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 104 LEU 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 48 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 261 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN F 209 ASN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 ASN O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 209 ASN ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.065002 restraints weight = 66307.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.067162 restraints weight = 31922.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.068614 restraints weight = 19421.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.069568 restraints weight = 13520.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.070280 restraints weight = 10364.024| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24666 Z= 0.112 Angle : 0.608 10.778 33564 Z= 0.299 Chirality : 0.041 0.187 3606 Planarity : 0.004 0.052 4518 Dihedral : 3.829 15.558 3372 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.29 % Allowed : 16.47 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.15), residues: 3090 helix: 0.95 (0.26), residues: 426 sheet: 0.38 (0.16), residues: 1050 loop : -0.87 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 219 TYR 0.017 0.001 TYR G 113 PHE 0.020 0.001 PHE Q 91 TRP 0.013 0.001 TRP D 23 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00254 (24660) covalent geometry : angle 0.60846 (33564) hydrogen bonds : bond 0.03480 ( 840) hydrogen bonds : angle 5.08768 ( 2538) Misc. bond : bond 0.00572 ( 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 523 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 466 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8307 (m) REVERT: A 55 ASN cc_start: 0.9291 (m-40) cc_final: 0.8985 (m-40) REVERT: A 59 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 99 ARG cc_start: 0.8694 (mtp85) cc_final: 0.8422 (mtt90) REVERT: A 112 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8309 (mttt) REVERT: A 125 MET cc_start: 0.8737 (mmm) cc_final: 0.8403 (tpp) REVERT: B 15 GLU cc_start: 0.8321 (mp0) cc_final: 0.7897 (mp0) REVERT: B 31 GLU cc_start: 0.7910 (tp30) cc_final: 0.7542 (tp30) REVERT: B 78 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8336 (mtpp) REVERT: C 198 TYR cc_start: 0.9246 (m-80) cc_final: 0.9005 (m-80) REVERT: C 215 LYS cc_start: 0.9611 (tttt) cc_final: 0.9372 (tttm) REVERT: C 236 MET cc_start: 0.8794 (mmt) cc_final: 0.7850 (mmm) REVERT: D 18 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8317 (m) REVERT: D 55 ASN cc_start: 0.9211 (m-40) cc_final: 0.8835 (m-40) REVERT: D 112 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8435 (mttt) REVERT: D 127 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8812 (ttmt) REVERT: E 15 GLU cc_start: 0.8161 (mp0) cc_final: 0.7650 (mp0) REVERT: E 31 GLU cc_start: 0.7742 (tp30) cc_final: 0.7529 (tp30) REVERT: E 34 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.7030 (tp) REVERT: E 78 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8244 (mtpp) REVERT: E 119 GLU cc_start: 0.7927 (mp0) cc_final: 0.7692 (mp0) REVERT: E 136 TYR cc_start: 0.9027 (m-80) cc_final: 0.8819 (m-80) REVERT: F 213 GLU cc_start: 0.8513 (tt0) cc_final: 0.8202 (tt0) REVERT: F 236 MET cc_start: 0.8648 (mmm) cc_final: 0.8371 (mmm) REVERT: G 79 GLU cc_start: 0.8239 (mp0) cc_final: 0.7950 (mt-10) REVERT: G 112 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8490 (mttt) REVERT: H 78 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8275 (mtpp) REVERT: H 84 MET cc_start: 0.9342 (mmp) cc_final: 0.9117 (mmm) REVERT: H 136 TYR cc_start: 0.8677 (m-80) cc_final: 0.8327 (m-80) REVERT: I 215 LYS cc_start: 0.9646 (tttt) cc_final: 0.9393 (tttm) REVERT: I 236 MET cc_start: 0.8695 (mmm) cc_final: 0.8428 (mmp) REVERT: J 18 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8316 (m) REVERT: J 55 ASN cc_start: 0.9283 (m-40) cc_final: 0.8972 (m-40) REVERT: J 99 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8397 (mtt90) REVERT: J 112 LYS cc_start: 0.9110 (mmtt) cc_final: 0.8300 (mttt) REVERT: J 125 MET cc_start: 0.8739 (mmm) cc_final: 0.8425 (tpp) REVERT: K 31 GLU cc_start: 0.7873 (tp30) cc_final: 0.7637 (tp30) REVERT: K 78 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8324 (mtpp) REVERT: L 215 LYS cc_start: 0.9613 (tttt) cc_final: 0.9373 (tttm) REVERT: L 236 MET cc_start: 0.8796 (mmt) cc_final: 0.7847 (mmm) REVERT: M 18 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8305 (m) REVERT: M 55 ASN cc_start: 0.9198 (m-40) cc_final: 0.8841 (m-40) REVERT: M 112 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8443 (mttt) REVERT: M 127 LYS cc_start: 0.8939 (ttmm) cc_final: 0.8640 (ttmt) REVERT: N 15 GLU cc_start: 0.8043 (mp0) cc_final: 0.7502 (mp0) REVERT: N 34 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7035 (tp) REVERT: N 57 ASP cc_start: 0.7988 (t0) cc_final: 0.7582 (t0) REVERT: N 78 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8242 (mtpp) REVERT: N 119 GLU cc_start: 0.8006 (mp0) cc_final: 0.7739 (mp0) REVERT: O 213 GLU cc_start: 0.8605 (tt0) cc_final: 0.8335 (tt0) REVERT: O 236 MET cc_start: 0.8819 (mmt) cc_final: 0.8134 (mmm) REVERT: O 238 MET cc_start: 0.8416 (tpp) cc_final: 0.8037 (tpp) REVERT: P 18 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.7671 (m) REVERT: P 79 GLU cc_start: 0.8221 (mp0) cc_final: 0.8001 (mt-10) REVERT: P 112 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8509 (mttt) REVERT: Q 15 GLU cc_start: 0.8138 (mp0) cc_final: 0.7909 (mp0) REVERT: Q 78 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8265 (mtpp) REVERT: Q 84 MET cc_start: 0.9372 (mmp) cc_final: 0.9143 (mmm) REVERT: Q 136 TYR cc_start: 0.8658 (m-80) cc_final: 0.8302 (m-80) REVERT: R 64 GLN cc_start: 0.8151 (mp10) cc_final: 0.7819 (mp10) REVERT: R 215 LYS cc_start: 0.9643 (tttt) cc_final: 0.9385 (tttm) outliers start: 57 outliers final: 32 residues processed: 494 average time/residue: 0.1622 time to fit residues: 122.5761 Evaluate side-chains 483 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 444 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR 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 80 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 80 VAL 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 63 LEU Chi-restraints excluded: chain J residue 126 CYS 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 M residue 18 THR Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 38 LEU 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 45 SER Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain R residue 80 VAL 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 228 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 282 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 292 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.074368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.064046 restraints weight = 67373.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.066127 restraints weight = 32969.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.067511 restraints weight = 20120.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.068448 restraints weight = 14063.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.069086 restraints weight = 10787.354| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24666 Z= 0.239 Angle : 0.675 19.514 33564 Z= 0.334 Chirality : 0.043 0.495 3606 Planarity : 0.005 0.053 4518 Dihedral : 4.029 15.890 3372 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.09 % Allowed : 16.35 % Favored : 80.56 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 3090 helix: 0.51 (0.26), residues: 426 sheet: 0.29 (0.16), residues: 1056 loop : -0.85 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 27 TYR 0.018 0.002 TYR I 198 PHE 0.017 0.002 PHE O 121 TRP 0.066 0.003 TRP P 23 HIS 0.004 0.001 HIS Q 120 Details of bonding type rmsd covalent geometry : bond 0.00541 (24660) covalent geometry : angle 0.67512 (33564) hydrogen bonds : bond 0.04129 ( 840) hydrogen bonds : angle 5.17685 ( 2538) Misc. bond : bond 0.00717 ( 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 505 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 428 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8197 (m) REVERT: A 55 ASN cc_start: 0.9281 (m-40) cc_final: 0.8986 (m-40) REVERT: A 99 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8467 (mtt90) REVERT: A 112 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8370 (mttt) REVERT: A 125 MET cc_start: 0.8776 (mmm) cc_final: 0.8458 (tpp) REVERT: B 31 GLU cc_start: 0.7887 (tp30) cc_final: 0.7591 (tp30) REVERT: B 78 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8300 (mtpp) REVERT: C 125 ILE cc_start: 0.9239 (mm) cc_final: 0.8913 (pt) REVERT: C 198 TYR cc_start: 0.9229 (m-80) cc_final: 0.8982 (m-80) REVERT: C 215 LYS cc_start: 0.9663 (tttt) cc_final: 0.9420 (tttm) REVERT: C 236 MET cc_start: 0.8823 (mmt) cc_final: 0.7897 (mmm) REVERT: D 18 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8239 (m) REVERT: D 55 ASN cc_start: 0.9186 (m-40) cc_final: 0.8830 (m-40) REVERT: D 112 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8506 (mttt) REVERT: E 15 GLU cc_start: 0.8019 (mp0) cc_final: 0.7291 (mp0) REVERT: E 57 ASP cc_start: 0.7961 (t0) cc_final: 0.7736 (t0) REVERT: E 78 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8250 (mtpp) REVERT: E 119 GLU cc_start: 0.7964 (mp0) cc_final: 0.7730 (mp0) REVERT: F 236 MET cc_start: 0.8695 (mmm) cc_final: 0.8385 (mmm) REVERT: G 18 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7431 (m) REVERT: G 79 GLU cc_start: 0.8217 (mp0) cc_final: 0.7565 (mp0) REVERT: G 112 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8550 (mttt) REVERT: H 78 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8284 (mtpp) REVERT: H 136 TYR cc_start: 0.8733 (m-80) cc_final: 0.8401 (m-80) REVERT: I 215 LYS cc_start: 0.9661 (tttt) cc_final: 0.9376 (tttm) REVERT: J 18 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8168 (m) REVERT: J 55 ASN cc_start: 0.9279 (m-40) cc_final: 0.8987 (m-40) REVERT: J 112 LYS cc_start: 0.9150 (mmtt) cc_final: 0.8425 (mttt) REVERT: J 125 MET cc_start: 0.8768 (mmm) cc_final: 0.8469 (tpp) REVERT: K 78 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8299 (mtpp) REVERT: L 110 ASP cc_start: 0.8050 (t0) cc_final: 0.7846 (t0) REVERT: L 215 LYS cc_start: 0.9664 (tttt) cc_final: 0.9420 (tttm) REVERT: L 236 MET cc_start: 0.8829 (mmt) cc_final: 0.7904 (mmm) REVERT: M 18 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8220 (m) REVERT: M 55 ASN cc_start: 0.9174 (m-40) cc_final: 0.8828 (m-40) REVERT: M 112 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8522 (mttt) REVERT: M 127 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8584 (ttmt) REVERT: N 15 GLU cc_start: 0.8031 (mp0) cc_final: 0.7327 (mp0) REVERT: N 57 ASP cc_start: 0.8000 (t0) cc_final: 0.7722 (m-30) REVERT: N 78 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8257 (mtpp) REVERT: N 119 GLU cc_start: 0.7967 (mp0) cc_final: 0.7677 (mp0) REVERT: O 213 GLU cc_start: 0.8560 (tt0) cc_final: 0.8268 (tt0) REVERT: O 236 MET cc_start: 0.8865 (mmt) cc_final: 0.8210 (mmm) REVERT: O 238 MET cc_start: 0.8412 (tpp) cc_final: 0.8128 (tpp) REVERT: P 18 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7423 (m) REVERT: P 79 GLU cc_start: 0.8236 (mp0) cc_final: 0.7577 (mp0) REVERT: P 112 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8518 (mttt) REVERT: Q 15 GLU cc_start: 0.8154 (mp0) cc_final: 0.7723 (mp0) REVERT: Q 78 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8350 (mtpp) REVERT: Q 136 TYR cc_start: 0.8728 (m-80) cc_final: 0.8390 (m-80) REVERT: R 215 LYS cc_start: 0.9664 (tttt) cc_final: 0.9369 (tttm) outliers start: 77 outliers final: 49 residues processed: 471 average time/residue: 0.1835 time to fit residues: 132.6793 Evaluate side-chains 472 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 417 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 33 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 126 CYS 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 45 SER 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 63 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 26 MET 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 126 THR Chi-restraints excluded: chain M residue 18 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 38 LEU 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 45 SER 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 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 259 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 242 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 297 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 209 ASN F 86 ASN ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.076452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.065939 restraints weight = 67055.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.068109 restraints weight = 32398.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.069559 restraints weight = 19693.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.070539 restraints weight = 13662.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.071200 restraints weight = 10399.055| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.218 24666 Z= 0.131 Angle : 0.653 23.144 33564 Z= 0.319 Chirality : 0.041 0.246 3606 Planarity : 0.005 0.052 4518 Dihedral : 3.910 26.145 3372 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 2.21 % Allowed : 17.31 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3090 helix: 0.51 (0.26), residues: 426 sheet: 0.35 (0.16), residues: 1050 loop : -0.79 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 219 TYR 0.025 0.001 TYR P 113 PHE 0.016 0.001 PHE Q 91 TRP 0.090 0.002 TRP J 23 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00308 (24660) covalent geometry : angle 0.65331 (33564) hydrogen bonds : bond 0.03546 ( 840) hydrogen bonds : angle 5.14184 ( 2538) Misc. bond : bond 0.01193 ( 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 504 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 449 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8216 (m) REVERT: A 55 ASN cc_start: 0.9273 (m-40) cc_final: 0.8970 (m-40) REVERT: A 99 ARG cc_start: 0.8693 (mtp85) cc_final: 0.8404 (mtt90) REVERT: A 112 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8343 (mttt) REVERT: A 125 MET cc_start: 0.8729 (mmm) cc_final: 0.8411 (tpp) REVERT: B 31 GLU cc_start: 0.7875 (tp30) cc_final: 0.7548 (tp30) REVERT: B 78 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8188 (mtpp) REVERT: C 198 TYR cc_start: 0.9248 (m-80) cc_final: 0.9016 (m-80) REVERT: C 215 LYS cc_start: 0.9629 (tttt) cc_final: 0.9390 (tttm) REVERT: C 236 MET cc_start: 0.8801 (mmt) cc_final: 0.7855 (mmm) REVERT: D 18 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8306 (m) REVERT: D 55 ASN cc_start: 0.9193 (m-40) cc_final: 0.8826 (m-40) REVERT: D 112 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8406 (mttt) REVERT: E 15 GLU cc_start: 0.7958 (mp0) cc_final: 0.7575 (mp0) REVERT: E 31 GLU cc_start: 0.7701 (tp30) cc_final: 0.7480 (tp30) REVERT: E 34 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6916 (tp) REVERT: E 57 ASP cc_start: 0.7938 (t0) cc_final: 0.7669 (t0) REVERT: E 78 LYS cc_start: 0.8565 (mtpt) cc_final: 0.8218 (mtpp) REVERT: F 236 MET cc_start: 0.8681 (mmm) cc_final: 0.8403 (mmm) REVERT: G 18 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7440 (m) REVERT: G 79 GLU cc_start: 0.8221 (mp0) cc_final: 0.7932 (mt-10) REVERT: G 112 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8564 (mttt) REVERT: H 78 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8254 (mtpp) REVERT: H 136 TYR cc_start: 0.8686 (m-80) cc_final: 0.8374 (m-80) REVERT: I 215 LYS cc_start: 0.9651 (tttt) cc_final: 0.9300 (tttm) REVERT: J 18 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8165 (m) REVERT: J 55 ASN cc_start: 0.9272 (m-40) cc_final: 0.8965 (m-40) REVERT: J 99 ARG cc_start: 0.8710 (mtp85) cc_final: 0.8455 (mtt90) REVERT: J 112 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8338 (mttt) REVERT: J 125 MET cc_start: 0.8731 (mmm) cc_final: 0.8424 (tpp) REVERT: K 78 LYS cc_start: 0.8559 (mtpt) cc_final: 0.8192 (mtpp) REVERT: L 215 LYS cc_start: 0.9623 (tttt) cc_final: 0.9376 (tttm) REVERT: L 236 MET cc_start: 0.8807 (mmt) cc_final: 0.7862 (mmm) REVERT: M 18 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8311 (m) REVERT: M 55 ASN cc_start: 0.9186 (m-40) cc_final: 0.8828 (m-40) REVERT: M 112 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8423 (mttt) REVERT: M 127 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8619 (ttmt) REVERT: N 15 GLU cc_start: 0.7992 (mp0) cc_final: 0.7513 (mp0) REVERT: N 34 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6946 (tp) REVERT: N 57 ASP cc_start: 0.7962 (t0) cc_final: 0.7555 (t0) REVERT: N 78 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8223 (mtpp) REVERT: N 119 GLU cc_start: 0.7992 (mp0) cc_final: 0.7704 (mp0) REVERT: O 213 GLU cc_start: 0.8580 (tt0) cc_final: 0.8303 (tt0) REVERT: O 236 MET cc_start: 0.8870 (mmt) cc_final: 0.8140 (mmm) REVERT: O 238 MET cc_start: 0.8392 (tpp) cc_final: 0.8023 (tpp) REVERT: P 18 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7416 (m) REVERT: P 79 GLU cc_start: 0.8216 (mp0) cc_final: 0.7959 (mt-10) REVERT: P 112 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8600 (mttt) REVERT: Q 15 GLU cc_start: 0.8019 (mp0) cc_final: 0.7682 (mp0) REVERT: Q 78 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8298 (mtpp) REVERT: Q 136 TYR cc_start: 0.8679 (m-80) cc_final: 0.8348 (m-80) REVERT: R 215 LYS cc_start: 0.9645 (tttt) cc_final: 0.9289 (tttm) outliers start: 55 outliers final: 37 residues processed: 482 average time/residue: 0.1866 time to fit residues: 137.4768 Evaluate side-chains 481 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 436 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 80 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 34 ILE 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 45 SER Chi-restraints excluded: chain H residue 37 GLU Chi-restraints excluded: chain I residue 80 VAL 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 63 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 26 MET 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 M residue 18 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 126 THR Chi-restraints excluded: chain O residue 150 ASN Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 45 SER 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 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 2 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.074521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.064094 restraints weight = 67367.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.066173 restraints weight = 33225.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.067588 restraints weight = 20434.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.068546 restraints weight = 14300.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.069180 restraints weight = 10949.275| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 24666 Z= 0.223 Angle : 0.715 16.031 33564 Z= 0.356 Chirality : 0.042 0.390 3606 Planarity : 0.005 0.052 4518 Dihedral : 4.021 23.816 3372 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.21 % Allowed : 17.31 % Favored : 80.48 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.15), residues: 3090 helix: 0.37 (0.26), residues: 426 sheet: 0.29 (0.16), residues: 1056 loop : -0.77 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 104 TYR 0.021 0.002 TYR P 113 PHE 0.017 0.001 PHE R 121 TRP 0.087 0.003 TRP G 23 HIS 0.003 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00518 (24660) covalent geometry : angle 0.71460 (33564) hydrogen bonds : bond 0.04364 ( 840) hydrogen bonds : angle 5.18080 ( 2538) Misc. bond : bond 0.01465 ( 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 482 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 427 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.7799 (m) REVERT: A 55 ASN cc_start: 0.9286 (m-40) cc_final: 0.8985 (m-40) REVERT: A 112 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8351 (mttt) REVERT: A 125 MET cc_start: 0.8761 (mmm) cc_final: 0.8450 (tpp) REVERT: B 14 GLU cc_start: 0.8147 (pm20) cc_final: 0.7705 (pm20) REVERT: B 15 GLU cc_start: 0.8290 (mp0) cc_final: 0.7763 (mp0) REVERT: B 31 GLU cc_start: 0.7893 (tp30) cc_final: 0.7609 (tp30) REVERT: B 78 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8254 (mtpp) REVERT: C 198 TYR cc_start: 0.9231 (m-80) cc_final: 0.8998 (m-80) REVERT: C 215 LYS cc_start: 0.9658 (tttt) cc_final: 0.9419 (tttm) REVERT: C 236 MET cc_start: 0.8826 (mmt) cc_final: 0.7912 (mmm) REVERT: D 18 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8229 (m) REVERT: D 55 ASN cc_start: 0.9191 (m-40) cc_final: 0.8837 (m-40) REVERT: D 112 LYS cc_start: 0.9014 (mmtt) cc_final: 0.8418 (mttt) REVERT: E 15 GLU cc_start: 0.7965 (mp0) cc_final: 0.7512 (mp0) REVERT: E 34 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6986 (tp) REVERT: E 78 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8317 (mtpp) REVERT: F 236 MET cc_start: 0.8716 (mmm) cc_final: 0.8414 (mmm) REVERT: G 18 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7363 (m) REVERT: G 79 GLU cc_start: 0.8232 (mp0) cc_final: 0.7922 (mt-10) REVERT: G 112 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8559 (mttt) REVERT: H 78 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8257 (mtpp) REVERT: H 136 TYR cc_start: 0.8722 (m-80) cc_final: 0.8408 (m-80) REVERT: I 215 LYS cc_start: 0.9663 (tttt) cc_final: 0.9376 (tttm) REVERT: J 18 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.7795 (m) REVERT: J 55 ASN cc_start: 0.9283 (m-40) cc_final: 0.8994 (m-40) REVERT: J 99 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8473 (mtt90) REVERT: J 112 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8377 (mttt) REVERT: J 125 MET cc_start: 0.8765 (mmm) cc_final: 0.8471 (tpp) REVERT: K 78 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8246 (mtpp) REVERT: L 110 ASP cc_start: 0.8134 (t0) cc_final: 0.7876 (t0) REVERT: L 215 LYS cc_start: 0.9658 (tttt) cc_final: 0.9415 (tttm) REVERT: L 236 MET cc_start: 0.8831 (mmt) cc_final: 0.7917 (mmm) REVERT: M 18 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8224 (m) REVERT: M 55 ASN cc_start: 0.9159 (m-40) cc_final: 0.8809 (m-40) REVERT: M 112 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8433 (mttt) REVERT: M 127 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8581 (ttmt) REVERT: N 15 GLU cc_start: 0.7989 (mp0) cc_final: 0.7419 (mp0) REVERT: N 34 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.7018 (tp) REVERT: N 57 ASP cc_start: 0.7996 (t0) cc_final: 0.7599 (t0) REVERT: N 78 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8322 (mtpp) REVERT: N 119 GLU cc_start: 0.7977 (mp0) cc_final: 0.7719 (mp0) REVERT: O 213 GLU cc_start: 0.8591 (tt0) cc_final: 0.8295 (tt0) REVERT: O 236 MET cc_start: 0.8872 (mmt) cc_final: 0.8125 (mmm) REVERT: O 238 MET cc_start: 0.8442 (tpp) cc_final: 0.8119 (tpp) REVERT: P 18 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7341 (m) REVERT: P 79 GLU cc_start: 0.8236 (mp0) cc_final: 0.7599 (mp0) REVERT: P 112 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8616 (mttt) REVERT: Q 15 GLU cc_start: 0.8155 (mp0) cc_final: 0.7847 (mp0) REVERT: Q 78 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8310 (mtpp) REVERT: Q 136 TYR cc_start: 0.8717 (m-80) cc_final: 0.8389 (m-80) REVERT: R 215 LYS cc_start: 0.9662 (tttt) cc_final: 0.9375 (tttm) outliers start: 55 outliers final: 40 residues processed: 463 average time/residue: 0.1866 time to fit residues: 132.1495 Evaluate side-chains 469 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 421 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 80 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 45 SER Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 34 ILE 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 45 SER Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 38 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 63 LEU Chi-restraints excluded: chain J residue 126 CYS Chi-restraints excluded: chain K residue 26 MET 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 M residue 18 THR Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 126 CYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 38 LEU 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 45 SER Chi-restraints excluded: chain Q residue 38 LEU 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 271 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 ASN ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.076085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.065696 restraints weight = 65765.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.067814 restraints weight = 32023.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.069229 restraints weight = 19585.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.070200 restraints weight = 13653.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.070825 restraints weight = 10420.531| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.163 24666 Z= 0.145 Angle : 0.742 26.493 33564 Z= 0.361 Chirality : 0.042 0.300 3606 Planarity : 0.005 0.052 4518 Dihedral : 3.952 20.380 3372 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.93 % Allowed : 17.51 % Favored : 80.56 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3090 helix: 0.46 (0.26), residues: 426 sheet: 0.36 (0.16), residues: 1056 loop : -0.73 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 219 TYR 0.021 0.001 TYR P 113 PHE 0.016 0.001 PHE Q 91 TRP 0.059 0.002 TRP G 23 HIS 0.003 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00331 (24660) covalent geometry : angle 0.74227 (33564) hydrogen bonds : bond 0.03874 ( 840) hydrogen bonds : angle 5.12084 ( 2538) Misc. bond : bond 0.01327 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3590.38 seconds wall clock time: 63 minutes 3.22 seconds (3783.22 seconds total)