Starting phenix.real_space_refine on Thu Jan 23 22:56:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ceo_45505/01_2025/9ceo_45505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ceo_45505/01_2025/9ceo_45505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ceo_45505/01_2025/9ceo_45505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ceo_45505/01_2025/9ceo_45505.map" model { file = "/net/cci-nas-00/data/ceres_data/9ceo_45505/01_2025/9ceo_45505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ceo_45505/01_2025/9ceo_45505.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.111 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 114 5.16 5 C 45030 2.51 5 N 12730 2.21 5 O 15542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 393 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 73416 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "B" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "C" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "D" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "E" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "F" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "G" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "H" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "I" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "J" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "K" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "L" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "M" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "N" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "O" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "P" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Q" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "R" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "S" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "T" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "U" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "V" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "W" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "X" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Y" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "Z" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "a" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "b" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "c" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "d" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "e" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "f" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "g" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "h" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "i" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "j" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "k" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Chain: "l" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1932 Classifications: {'peptide': 270} Link IDs: {'TRANS': 269} Time building chain proxies: 31.47, per 1000 atoms: 0.43 Number of scatterers: 73416 At special positions: 0 Unit cell: (138.444, 139.278, 335.268, 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 114 16.00 O 15542 8.00 N 12730 7.00 C 45030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.19 Conformation dependent library (CDL) restraints added in 7.9 seconds 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18924 Finding SS restraints... Secondary structure from input PDB file: 273 helices and 38 sheets defined 75.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 Processing helix chain 'A' and resid 45 through 61 Processing helix chain 'A' and resid 61 through 101 removed outlier: 4.187A pdb=" N VAL A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 Processing helix chain 'A' and resid 179 through 234 removed outlier: 4.084A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 263 removed outlier: 3.697A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.556A pdb=" N SER A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 270 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 36 Processing helix chain 'B' and resid 45 through 61 Processing helix chain 'B' and resid 61 through 102 removed outlier: 4.177A pdb=" N VAL B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 Processing helix chain 'B' and resid 179 through 234 removed outlier: 3.999A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 263 removed outlier: 3.533A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.832A pdb=" N ILE B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 270 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 61 through 101 removed outlier: 4.168A pdb=" N VAL C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 Processing helix chain 'C' and resid 179 through 234 removed outlier: 4.046A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.844A pdb=" N GLU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 270 removed outlier: 3.624A pdb=" N SER C 267 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 36 Processing helix chain 'D' and resid 45 through 61 Processing helix chain 'D' and resid 61 through 101 removed outlier: 4.117A pdb=" N VAL D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 Processing helix chain 'D' and resid 179 through 234 removed outlier: 3.800A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 4.106A pdb=" N GLU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 270 removed outlier: 3.835A pdb=" N SER D 267 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 268 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 36 Processing helix chain 'E' and resid 45 through 61 Processing helix chain 'E' and resid 61 through 101 removed outlier: 4.287A pdb=" N VAL E 65 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 Processing helix chain 'E' and resid 179 through 234 removed outlier: 4.020A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.682A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 removed outlier: 4.173A pdb=" N SER E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 271' Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.667A pdb=" N LEU F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 61 Processing helix chain 'F' and resid 61 through 101 removed outlier: 4.231A pdb=" N VAL F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 Processing helix chain 'F' and resid 179 through 234 removed outlier: 4.002A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 263 removed outlier: 3.617A pdb=" N GLU F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 270 removed outlier: 3.689A pdb=" N SER F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE F 268 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.521A pdb=" N LEU G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 61 Processing helix chain 'G' and resid 61 through 102 removed outlier: 4.127A pdb=" N VAL G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 removed outlier: 3.560A pdb=" N THR G 125 " --> pdb=" O ARG G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 234 removed outlier: 4.011A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 4.093A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 272 removed outlier: 4.453A pdb=" N ILE G 268 " --> pdb=" O SER G 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU G 269 " --> pdb=" O SER G 265 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER G 270 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE G 272 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 264 through 272' Processing helix chain 'H' and resid 9 through 36 removed outlier: 3.517A pdb=" N LEU H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 61 removed outlier: 3.535A pdb=" N TRP H 49 " --> pdb=" O ASN H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 101 removed outlier: 4.383A pdb=" N VAL H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 130 removed outlier: 3.631A pdb=" N THR H 125 " --> pdb=" O ARG H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 234 removed outlier: 3.908A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 263 removed outlier: 4.036A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 271 removed outlier: 3.962A pdb=" N SER H 270 " --> pdb=" O SER H 266 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 266 through 271' Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.541A pdb=" N LEU I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 Processing helix chain 'I' and resid 61 through 101 removed outlier: 4.409A pdb=" N VAL I 65 " --> pdb=" O SER I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 Processing helix chain 'I' and resid 179 through 234 removed outlier: 3.850A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 263 removed outlier: 3.860A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 266 No H-bonds generated for 'chain 'I' and resid 264 through 266' Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.539A pdb=" N LEU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 36 removed outlier: 3.559A pdb=" N LEU J 13 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 Processing helix chain 'J' and resid 61 through 101 removed outlier: 4.195A pdb=" N VAL J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 Processing helix chain 'J' and resid 179 through 234 removed outlier: 3.842A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 264 removed outlier: 3.959A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER J 264 " --> pdb=" O ILE J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 270 removed outlier: 3.944A pdb=" N ILE J 268 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER J 270 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 36 removed outlier: 3.562A pdb=" N LEU K 13 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 61 Processing helix chain 'K' and resid 61 through 102 removed outlier: 4.223A pdb=" N VAL K 65 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 Processing helix chain 'K' and resid 165 through 170 Processing helix chain 'K' and resid 179 through 234 removed outlier: 3.723A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.686A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 272 removed outlier: 4.097A pdb=" N SER K 267 " --> pdb=" O SER K 264 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE K 268 " --> pdb=" O SER K 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.796A pdb=" N LEU L 13 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 Processing helix chain 'L' and resid 62 through 101 Processing helix chain 'L' and resid 106 through 130 Processing helix chain 'L' and resid 179 through 234 removed outlier: 3.825A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 removed outlier: 3.785A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 271 removed outlier: 4.317A pdb=" N SER L 270 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 266 through 271' Processing helix chain 'M' and resid 9 through 36 Processing helix chain 'M' and resid 45 through 61 Processing helix chain 'M' and resid 62 through 101 Processing helix chain 'M' and resid 106 through 130 Processing helix chain 'M' and resid 179 through 234 removed outlier: 3.721A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 263 removed outlier: 3.634A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 270 removed outlier: 4.134A pdb=" N SER M 267 " --> pdb=" O SER M 264 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE M 268 " --> pdb=" O SER M 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 36 removed outlier: 3.734A pdb=" N LEU N 13 " --> pdb=" O ASN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 Processing helix chain 'N' and resid 61 through 101 removed outlier: 4.042A pdb=" N VAL N 65 " --> pdb=" O SER N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 130 Processing helix chain 'N' and resid 179 through 234 removed outlier: 4.116A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 removed outlier: 3.744A pdb=" N ALA N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 271 removed outlier: 4.149A pdb=" N SER N 270 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU N 271 " --> pdb=" O SER N 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 266 through 271' Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.659A pdb=" N LEU O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 Processing helix chain 'O' and resid 61 through 101 removed outlier: 4.463A pdb=" N VAL O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 Processing helix chain 'O' and resid 179 through 234 removed outlier: 3.856A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 264 removed outlier: 3.807A pdb=" N GLU O 240 " --> pdb=" O ASP O 236 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 272 removed outlier: 3.630A pdb=" N ILE O 268 " --> pdb=" O SER O 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 36 removed outlier: 3.740A pdb=" N LEU P 13 " --> pdb=" O ASN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 61 Processing helix chain 'P' and resid 61 through 101 removed outlier: 4.309A pdb=" N VAL P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 Processing helix chain 'P' and resid 179 through 234 removed outlier: 3.886A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 264 removed outlier: 3.841A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 272 removed outlier: 3.642A pdb=" N ILE P 268 " --> pdb=" O SER P 265 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER P 270 " --> pdb=" O SER P 267 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE P 272 " --> pdb=" O LEU P 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.517A pdb=" N LEU Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 61 Processing helix chain 'Q' and resid 62 through 101 Processing helix chain 'Q' and resid 106 through 130 Processing helix chain 'Q' and resid 179 through 234 removed outlier: 3.816A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 264 removed outlier: 3.710A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER Q 264 " --> pdb=" O ILE Q 260 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 272 removed outlier: 3.636A pdb=" N ILE Q 268 " --> pdb=" O SER Q 265 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER Q 270 " --> pdb=" O SER Q 267 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE Q 272 " --> pdb=" O LEU Q 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.647A pdb=" N LEU R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 Processing helix chain 'R' and resid 61 through 101 removed outlier: 4.310A pdb=" N VAL R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 Processing helix chain 'R' and resid 179 through 234 removed outlier: 3.888A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 264 removed outlier: 3.623A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 270 removed outlier: 3.690A pdb=" N ILE R 268 " --> pdb=" O SER R 265 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.562A pdb=" N LEU S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 Processing helix chain 'S' and resid 61 through 102 removed outlier: 4.238A pdb=" N VAL S 65 " --> pdb=" O SER S 61 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP S 102 " --> pdb=" O LEU S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 Processing helix chain 'S' and resid 179 through 234 removed outlier: 3.925A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 263 removed outlier: 3.764A pdb=" N GLU S 240 " --> pdb=" O ASP S 236 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) Processing helix chain 'S' and resid 264 through 272 removed outlier: 3.563A pdb=" N ILE S 268 " --> pdb=" O SER S 265 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER S 270 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE S 272 " --> pdb=" O LEU S 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.554A pdb=" N LEU T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 61 Processing helix chain 'T' and resid 61 through 101 removed outlier: 4.306A pdb=" N VAL T 65 " --> pdb=" O SER T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 Processing helix chain 'T' and resid 179 through 234 removed outlier: 3.969A pdb=" N GLY T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 264 Processing helix chain 'T' and resid 265 through 272 removed outlier: 3.930A pdb=" N ILE T 268 " --> pdb=" O SER T 265 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER T 270 " --> pdb=" O SER T 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 36 removed outlier: 3.638A pdb=" N LEU U 13 " --> pdb=" O ASN U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 61 Processing helix chain 'U' and resid 61 through 101 removed outlier: 4.108A pdb=" N VAL U 65 " --> pdb=" O SER U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 130 Processing helix chain 'U' and resid 179 through 234 removed outlier: 3.866A pdb=" N GLY U 188 " --> pdb=" O LYS U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 236 through 264 removed outlier: 3.682A pdb=" N ALA U 242 " --> pdb=" O ALA U 238 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER U 264 " --> pdb=" O ILE U 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 272 removed outlier: 3.914A pdb=" N ILE U 268 " --> pdb=" O SER U 265 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER U 270 " --> pdb=" O SER U 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 36 removed outlier: 3.920A pdb=" N LEU V 13 " --> pdb=" O ASN V 9 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 61 Processing helix chain 'V' and resid 62 through 101 Processing helix chain 'V' and resid 106 through 130 Processing helix chain 'V' and resid 165 through 170 removed outlier: 3.525A pdb=" N LEU V 169 " --> pdb=" O LEU V 166 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY V 170 " --> pdb=" O GLY V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 179 through 234 removed outlier: 4.045A pdb=" N GLY V 188 " --> pdb=" O LYS V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 236 through 263 removed outlier: 3.554A pdb=" N GLU V 240 " --> pdb=" O ASP V 236 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 272 removed outlier: 3.785A pdb=" N ILE V 268 " --> pdb=" O SER V 265 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER V 270 " --> pdb=" O SER V 267 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE V 272 " --> pdb=" O LEU V 269 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 36 Processing helix chain 'W' and resid 45 through 61 Processing helix chain 'W' and resid 61 through 101 removed outlier: 4.233A pdb=" N VAL W 65 " --> pdb=" O SER W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 130 Processing helix chain 'W' and resid 179 through 234 removed outlier: 4.014A pdb=" N GLY W 188 " --> pdb=" O LYS W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 264 removed outlier: 3.521A pdb=" N GLU W 240 " --> pdb=" O ASP W 236 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA W 242 " --> pdb=" O ALA W 238 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER W 264 " --> pdb=" O ILE W 260 " (cutoff:3.500A) Processing helix chain 'W' and resid 265 through 272 removed outlier: 3.810A pdb=" N ILE W 268 " --> pdb=" O SER W 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER W 270 " --> pdb=" O SER W 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE W 272 " --> pdb=" O LEU W 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 36 Processing helix chain 'X' and resid 45 through 61 Processing helix chain 'X' and resid 61 through 101 removed outlier: 4.076A pdb=" N VAL X 65 " --> pdb=" O SER X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 130 Processing helix chain 'X' and resid 179 through 234 removed outlier: 3.839A pdb=" N GLY X 188 " --> pdb=" O LYS X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 264 removed outlier: 3.587A pdb=" N GLU X 240 " --> pdb=" O ASP X 236 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA X 242 " --> pdb=" O ALA X 238 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER X 264 " --> pdb=" O ILE X 260 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 270 removed outlier: 4.041A pdb=" N ILE X 268 " --> pdb=" O SER X 265 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER X 270 " --> pdb=" O SER X 267 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 36 removed outlier: 3.622A pdb=" N LEU Y 13 " --> pdb=" O ASN Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 Processing helix chain 'Y' and resid 61 through 101 removed outlier: 4.159A pdb=" N VAL Y 65 " --> pdb=" O SER Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 130 Processing helix chain 'Y' and resid 165 through 170 Processing helix chain 'Y' and resid 179 through 234 removed outlier: 3.896A pdb=" N GLY Y 188 " --> pdb=" O LYS Y 184 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 263 removed outlier: 3.620A pdb=" N GLU Y 240 " --> pdb=" O ASP Y 236 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA Y 242 " --> pdb=" O ALA Y 238 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 270 removed outlier: 3.687A pdb=" N SER Y 267 " --> pdb=" O SER Y 264 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE Y 268 " --> pdb=" O SER Y 265 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 36 removed outlier: 3.682A pdb=" N LEU Z 13 " --> pdb=" O ASN Z 9 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 61 Processing helix chain 'Z' and resid 61 through 101 removed outlier: 4.046A pdb=" N VAL Z 65 " --> pdb=" O SER Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 130 Processing helix chain 'Z' and resid 179 through 234 removed outlier: 3.794A pdb=" N GLY Z 188 " --> pdb=" O LYS Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 236 through 263 removed outlier: 3.701A pdb=" N GLU Z 240 " --> pdb=" O ASP Z 236 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA Z 242 " --> pdb=" O ALA Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 272 removed outlier: 3.633A pdb=" N SER Z 267 " --> pdb=" O SER Z 264 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE Z 268 " --> pdb=" O SER Z 265 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER Z 270 " --> pdb=" O SER Z 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 36 removed outlier: 3.726A pdb=" N LEU a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 61 Processing helix chain 'a' and resid 61 through 101 removed outlier: 4.214A pdb=" N VAL a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 106 through 130 Processing helix chain 'a' and resid 165 through 170 Processing helix chain 'a' and resid 179 through 234 removed outlier: 3.961A pdb=" N GLY a 188 " --> pdb=" O LYS a 184 " (cutoff:3.500A) Processing helix chain 'a' and resid 236 through 263 removed outlier: 3.615A pdb=" N GLU a 240 " --> pdb=" O ASP a 236 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA a 242 " --> pdb=" O ALA a 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 264 through 272 removed outlier: 3.690A pdb=" N ILE a 268 " --> pdb=" O SER a 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER a 270 " --> pdb=" O SER a 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 36 Processing helix chain 'b' and resid 45 through 61 Processing helix chain 'b' and resid 61 through 101 removed outlier: 4.093A pdb=" N VAL b 65 " --> pdb=" O SER b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 130 Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.699A pdb=" N GLY b 170 " --> pdb=" O GLY b 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 234 removed outlier: 4.105A pdb=" N GLY b 188 " --> pdb=" O LYS b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 236 through 263 removed outlier: 3.702A pdb=" N GLU b 240 " --> pdb=" O ASP b 236 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA b 242 " --> pdb=" O ALA b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 272 removed outlier: 3.506A pdb=" N SER b 267 " --> pdb=" O SER b 264 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE b 268 " --> pdb=" O SER b 265 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER b 270 " --> pdb=" O SER b 267 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 36 Processing helix chain 'c' and resid 45 through 61 Processing helix chain 'c' and resid 61 through 101 removed outlier: 4.154A pdb=" N VAL c 65 " --> pdb=" O SER c 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 130 Processing helix chain 'c' and resid 179 through 234 removed outlier: 3.998A pdb=" N GLY c 188 " --> pdb=" O LYS c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 263 removed outlier: 3.592A pdb=" N GLU c 240 " --> pdb=" O ASP c 236 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA c 242 " --> pdb=" O ALA c 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 264 through 272 removed outlier: 3.526A pdb=" N SER c 267 " --> pdb=" O SER c 264 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE c 268 " --> pdb=" O SER c 265 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER c 270 " --> pdb=" O SER c 267 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE c 272 " --> pdb=" O LEU c 269 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 36 removed outlier: 3.551A pdb=" N LEU d 13 " --> pdb=" O ASN d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 61 Processing helix chain 'd' and resid 61 through 101 removed outlier: 4.104A pdb=" N VAL d 65 " --> pdb=" O SER d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 130 Processing helix chain 'd' and resid 165 through 170 removed outlier: 3.568A pdb=" N LEU d 169 " --> pdb=" O LEU d 166 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY d 170 " --> pdb=" O GLY d 167 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 234 removed outlier: 4.090A pdb=" N GLY d 188 " --> pdb=" O LYS d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 263 removed outlier: 3.989A pdb=" N ALA d 242 " --> pdb=" O ALA d 238 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 272 removed outlier: 3.644A pdb=" N SER d 267 " --> pdb=" O SER d 264 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE d 268 " --> pdb=" O SER d 265 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER d 270 " --> pdb=" O SER d 267 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 36 Processing helix chain 'e' and resid 45 through 61 Processing helix chain 'e' and resid 61 through 102 removed outlier: 3.987A pdb=" N VAL e 65 " --> pdb=" O SER e 61 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP e 102 " --> pdb=" O LEU e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 130 Processing helix chain 'e' and resid 179 through 234 removed outlier: 3.737A pdb=" N GLY e 188 " --> pdb=" O LYS e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 236 through 263 removed outlier: 3.599A pdb=" N GLU e 240 " --> pdb=" O ASP e 236 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA e 242 " --> pdb=" O ALA e 238 " (cutoff:3.500A) Processing helix chain 'e' and resid 264 through 272 removed outlier: 3.777A pdb=" N ILE e 268 " --> pdb=" O SER e 265 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER e 270 " --> pdb=" O SER e 267 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 36 Processing helix chain 'f' and resid 45 through 61 Processing helix chain 'f' and resid 61 through 102 removed outlier: 4.218A pdb=" N VAL f 65 " --> pdb=" O SER f 61 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP f 102 " --> pdb=" O LEU f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 130 Processing helix chain 'f' and resid 179 through 234 removed outlier: 4.008A pdb=" N GLY f 188 " --> pdb=" O LYS f 184 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 263 removed outlier: 3.805A pdb=" N GLU f 240 " --> pdb=" O ASP f 236 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA f 242 " --> pdb=" O ALA f 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 264 through 272 removed outlier: 3.783A pdb=" N ILE f 268 " --> pdb=" O SER f 265 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER f 270 " --> pdb=" O SER f 267 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 36 Processing helix chain 'g' and resid 45 through 61 Processing helix chain 'g' and resid 61 through 101 removed outlier: 4.220A pdb=" N VAL g 65 " --> pdb=" O SER g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 106 through 130 Processing helix chain 'g' and resid 179 through 234 removed outlier: 4.085A pdb=" N GLY g 188 " --> pdb=" O LYS g 184 " (cutoff:3.500A) Processing helix chain 'g' and resid 236 through 263 removed outlier: 3.523A pdb=" N GLU g 240 " --> pdb=" O ASP g 236 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA g 242 " --> pdb=" O ALA g 238 " (cutoff:3.500A) Processing helix chain 'g' and resid 264 through 272 removed outlier: 3.833A pdb=" N ILE g 268 " --> pdb=" O SER g 265 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER g 270 " --> pdb=" O SER g 267 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE g 272 " --> pdb=" O LEU g 269 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 36 removed outlier: 3.563A pdb=" N LEU h 13 " --> pdb=" O ASN h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 45 through 61 Processing helix chain 'h' and resid 61 through 101 removed outlier: 4.146A pdb=" N VAL h 65 " --> pdb=" O SER h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 130 Processing helix chain 'h' and resid 179 through 234 removed outlier: 3.994A pdb=" N GLY h 188 " --> pdb=" O LYS h 184 " (cutoff:3.500A) Processing helix chain 'h' and resid 236 through 263 removed outlier: 3.550A pdb=" N GLU h 240 " --> pdb=" O ASP h 236 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA h 242 " --> pdb=" O ALA h 238 " (cutoff:3.500A) Processing helix chain 'h' and resid 264 through 270 removed outlier: 3.502A pdb=" N SER h 267 " --> pdb=" O SER h 264 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE h 268 " --> pdb=" O SER h 265 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER h 270 " --> pdb=" O SER h 267 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 36 Processing helix chain 'i' and resid 45 through 61 Processing helix chain 'i' and resid 61 through 101 removed outlier: 4.143A pdb=" N VAL i 65 " --> pdb=" O SER i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 130 Processing helix chain 'i' and resid 179 through 234 removed outlier: 3.754A pdb=" N GLY i 188 " --> pdb=" O LYS i 184 " (cutoff:3.500A) Processing helix chain 'i' and resid 236 through 264 removed outlier: 3.592A pdb=" N GLU i 240 " --> pdb=" O ASP i 236 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA i 242 " --> pdb=" O ALA i 238 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER i 264 " --> pdb=" O ILE i 260 " (cutoff:3.500A) Processing helix chain 'i' and resid 265 through 272 removed outlier: 3.756A pdb=" N ILE i 268 " --> pdb=" O SER i 265 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER i 270 " --> pdb=" O SER i 267 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 36 Processing helix chain 'j' and resid 45 through 61 Processing helix chain 'j' and resid 61 through 101 removed outlier: 4.125A pdb=" N VAL j 65 " --> pdb=" O SER j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 130 Processing helix chain 'j' and resid 179 through 234 removed outlier: 3.996A pdb=" N GLY j 188 " --> pdb=" O LYS j 184 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 263 removed outlier: 3.538A pdb=" N GLU j 240 " --> pdb=" O ASP j 236 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA j 242 " --> pdb=" O ALA j 238 " (cutoff:3.500A) Processing helix chain 'j' and resid 264 through 272 removed outlier: 3.770A pdb=" N ILE j 268 " --> pdb=" O SER j 265 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER j 270 " --> pdb=" O SER j 267 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 36 Processing helix chain 'k' and resid 45 through 61 Processing helix chain 'k' and resid 61 through 101 removed outlier: 4.176A pdb=" N VAL k 65 " --> pdb=" O SER k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 106 through 130 Processing helix chain 'k' and resid 179 through 234 removed outlier: 4.085A pdb=" N GLY k 188 " --> pdb=" O LYS k 184 " (cutoff:3.500A) Processing helix chain 'k' and resid 236 through 263 removed outlier: 3.982A pdb=" N ALA k 242 " --> pdb=" O ALA k 238 " (cutoff:3.500A) Processing helix chain 'k' and resid 264 through 272 removed outlier: 3.757A pdb=" N ILE k 268 " --> pdb=" O SER k 265 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER k 270 " --> pdb=" O SER k 267 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 36 Processing helix chain 'l' and resid 45 through 61 Processing helix chain 'l' and resid 61 through 101 removed outlier: 4.124A pdb=" N VAL l 65 " --> pdb=" O SER l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 106 through 130 Processing helix chain 'l' and resid 179 through 234 removed outlier: 3.989A pdb=" N GLY l 188 " --> pdb=" O LYS l 184 " (cutoff:3.500A) Processing helix chain 'l' and resid 236 through 263 removed outlier: 3.519A pdb=" N GLU l 240 " --> pdb=" O ASP l 236 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA l 242 " --> pdb=" O ALA l 238 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 272 removed outlier: 3.824A pdb=" N ILE l 268 " --> pdb=" O SER l 265 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 149 Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 146 Processing sheet with id=AA4, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AA5, first strand: chain 'E' and resid 145 through 149 Processing sheet with id=AA6, first strand: chain 'F' and resid 145 through 149 Processing sheet with id=AA7, first strand: chain 'G' and resid 145 through 146 Processing sheet with id=AA8, first strand: chain 'H' and resid 145 through 146 Processing sheet with id=AA9, first strand: chain 'I' and resid 145 through 146 Processing sheet with id=AB1, first strand: chain 'J' and resid 145 through 149 Processing sheet with id=AB2, first strand: chain 'K' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 149 Processing sheet with id=AB4, first strand: chain 'M' and resid 145 through 149 Processing sheet with id=AB5, first strand: chain 'N' and resid 145 through 146 Processing sheet with id=AB6, first strand: chain 'O' and resid 145 through 149 Processing sheet with id=AB7, first strand: chain 'P' and resid 145 through 149 Processing sheet with id=AB8, first strand: chain 'Q' and resid 145 through 149 Processing sheet with id=AB9, first strand: chain 'R' and resid 145 through 146 Processing sheet with id=AC1, first strand: chain 'S' and resid 145 through 149 Processing sheet with id=AC2, first strand: chain 'T' and resid 145 through 146 Processing sheet with id=AC3, first strand: chain 'U' and resid 145 through 149 Processing sheet with id=AC4, first strand: chain 'V' and resid 145 through 149 removed outlier: 3.537A pdb=" N PHE V 148 " --> pdb=" O PHE V 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 145 through 146 Processing sheet with id=AC6, first strand: chain 'X' and resid 145 through 146 Processing sheet with id=AC7, first strand: chain 'Y' and resid 148 through 149 Processing sheet with id=AC8, first strand: chain 'Z' and resid 145 through 146 Processing sheet with id=AC9, first strand: chain 'a' and resid 145 through 149 Processing sheet with id=AD1, first strand: chain 'b' and resid 145 through 149 Processing sheet with id=AD2, first strand: chain 'c' and resid 145 through 149 Processing sheet with id=AD3, first strand: chain 'd' and resid 145 through 149 Processing sheet with id=AD4, first strand: chain 'e' and resid 145 through 149 Processing sheet with id=AD5, first strand: chain 'f' and resid 145 through 149 Processing sheet with id=AD6, first strand: chain 'g' and resid 145 through 146 Processing sheet with id=AD7, first strand: chain 'h' and resid 145 through 146 Processing sheet with id=AD8, first strand: chain 'i' and resid 145 through 149 Processing sheet with id=AD9, first strand: chain 'j' and resid 145 through 146 Processing sheet with id=AE1, first strand: chain 'k' and resid 145 through 149 Processing sheet with id=AE2, first strand: chain 'l' and resid 145 through 149 6565 hydrogen bonds defined for protein. 19359 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: 26.48 Time building geometry restraints manager: 17.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16747 1.33 - 1.45: 13478 1.45 - 1.57: 43343 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 73796 Sorted by residual: bond pdb=" CG1 ILE X 124 " pdb=" CD1 ILE X 124 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.85e+00 bond pdb=" N GLN T 17 " pdb=" CA GLN T 17 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.20e-02 6.94e+03 2.67e+00 bond pdb=" CG1 ILE a 190 " pdb=" CD1 ILE a 190 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.40e+00 bond pdb=" CG1 ILE U 124 " pdb=" CD1 ILE U 124 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.07e+00 bond pdb=" CG ASP X 77 " pdb=" OD1 ASP X 77 " ideal model delta sigma weight residual 1.249 1.222 0.027 1.90e-02 2.77e+03 1.99e+00 ... (remaining 73791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 98643 2.24 - 4.48: 1066 4.48 - 6.72: 131 6.72 - 8.96: 20 8.96 - 11.21: 4 Bond angle restraints: 99864 Sorted by residual: angle pdb=" CB MET U 93 " pdb=" CG MET U 93 " pdb=" SD MET U 93 " ideal model delta sigma weight residual 112.70 101.49 11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA MET U 93 " pdb=" CB MET U 93 " pdb=" CG MET U 93 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" C ASP K 122 " pdb=" N GLN K 123 " pdb=" CA GLN K 123 " ideal model delta sigma weight residual 121.58 114.63 6.95 1.95e+00 2.63e-01 1.27e+01 angle pdb=" CB MET d 93 " pdb=" CG MET d 93 " pdb=" SD MET d 93 " ideal model delta sigma weight residual 112.70 102.32 10.38 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N GLN I 31 " pdb=" CA GLN I 31 " pdb=" CB GLN I 31 " ideal model delta sigma weight residual 110.16 115.14 -4.98 1.48e+00 4.57e-01 1.13e+01 ... (remaining 99859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 41810 18.00 - 35.99: 2566 35.99 - 53.99: 355 53.99 - 71.99: 98 71.99 - 89.98: 87 Dihedral angle restraints: 44916 sinusoidal: 15770 harmonic: 29146 Sorted by residual: dihedral pdb=" CA GLN i 263 " pdb=" C GLN i 263 " pdb=" N SER i 264 " pdb=" CA SER i 264 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASN Z 45 " pdb=" C ASN Z 45 " pdb=" N GLY Z 46 " pdb=" CA GLY Z 46 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLN k 263 " pdb=" C GLN k 263 " pdb=" N SER k 264 " pdb=" CA SER k 264 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 44913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 11201 0.055 - 0.109: 1474 0.109 - 0.164: 162 0.164 - 0.218: 6 0.218 - 0.273: 1 Chirality restraints: 12844 Sorted by residual: chirality pdb=" CA GLN T 17 " pdb=" N GLN T 17 " pdb=" C GLN T 17 " pdb=" CB GLN T 17 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CG LEU I 26 " pdb=" CB LEU I 26 " pdb=" CD1 LEU I 26 " pdb=" CD2 LEU I 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE K 124 " pdb=" CA ILE K 124 " pdb=" CG1 ILE K 124 " pdb=" CG2 ILE K 124 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 12841 not shown) Planarity restraints: 12768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG i 121 " -0.179 9.50e-02 1.11e+02 8.04e-02 4.32e+00 pdb=" NE ARG i 121 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG i 121 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG i 121 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG i 121 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 134 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ASN L 134 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN L 134 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY L 135 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN Z 134 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ASN Z 134 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN Z 134 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY Z 135 " -0.010 2.00e-02 2.50e+03 ... (remaining 12765 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1004 2.68 - 3.23: 76687 3.23 - 3.79: 117309 3.79 - 4.34: 154482 4.34 - 4.90: 255402 Nonbonded interactions: 604884 Sorted by model distance: nonbonded pdb=" OG SER A 5 " pdb=" OD2 ASP B 234 " model vdw 2.121 3.040 nonbonded pdb=" NH1 ARG D 121 " pdb=" O ALA D 173 " model vdw 2.141 3.120 nonbonded pdb=" O GLN J 31 " pdb=" OG1 THR J 35 " model vdw 2.145 3.040 nonbonded pdb=" NE2 GLN P 73 " pdb=" OD1 ASP P 212 " model vdw 2.156 3.120 nonbonded pdb=" OG1 THR K 206 " pdb=" OD1 ASP N 116 " model vdw 2.158 3.040 ... (remaining 604879 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.490 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: 0.090 Extract box with map and model: 2.240 Check model and map are aligned: 0.430 Set scattering table: 0.510 Process input model: 126.430 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.880 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.003 0.066 73796 Z= 0.202 Angle : 0.650 11.205 99864 Z= 0.378 Chirality : 0.036 0.273 12844 Planarity : 0.004 0.080 12768 Dihedral : 12.758 89.981 25992 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.70 % Favored : 98.16 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.07), residues: 10184 helix: 0.11 (0.04), residues: 7524 sheet: -3.76 (0.18), residues: 380 loop : 1.28 (0.15), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 49 HIS 0.004 0.001 HIS h 214 PHE 0.028 0.002 PHE g 117 ARG 0.012 0.001 ARG d 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1060 time to evaluate : 6.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8108 (mt-10) REVERT: I 84 ASP cc_start: 0.6876 (m-30) cc_final: 0.6628 (m-30) REVERT: J 84 ASP cc_start: 0.8250 (m-30) cc_final: 0.7853 (m-30) REVERT: K 93 MET cc_start: 0.7220 (mtp) cc_final: 0.6939 (mtp) REVERT: L 4 ASN cc_start: 0.6630 (t0) cc_final: 0.6236 (t0) REVERT: M 38 LYS cc_start: 0.8046 (tptt) cc_final: 0.7797 (tptp) REVERT: N 208 SER cc_start: 0.8246 (t) cc_final: 0.7968 (p) REVERT: P 77 ASP cc_start: 0.8035 (m-30) cc_final: 0.7822 (m-30) REVERT: P 130 ASN cc_start: 0.7792 (m110) cc_final: 0.7458 (m110) REVERT: Q 126 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7281 (tttt) REVERT: R 240 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7431 (mm-30) REVERT: T 77 ASP cc_start: 0.7397 (m-30) cc_final: 0.7193 (m-30) REVERT: T 151 ASN cc_start: 0.8432 (t0) cc_final: 0.8200 (t0) REVERT: U 124 ILE cc_start: 0.7722 (mt) cc_final: 0.7448 (mt) REVERT: V 130 ASN cc_start: 0.7620 (m110) cc_final: 0.7168 (m110) REVERT: X 62 MET cc_start: 0.9099 (mmt) cc_final: 0.8893 (mmt) REVERT: b 29 VAL cc_start: 0.8099 (t) cc_final: 0.7822 (p) REVERT: f 28 GLN cc_start: 0.8195 (mm110) cc_final: 0.7989 (mp10) REVERT: g 67 ASP cc_start: 0.8175 (m-30) cc_final: 0.7959 (m-30) REVERT: h 88 ASP cc_start: 0.8461 (m-30) cc_final: 0.8181 (m-30) REVERT: i 252 GLN cc_start: 0.8514 (mm110) cc_final: 0.8232 (mm-40) REVERT: k 140 ASP cc_start: 0.8043 (t0) cc_final: 0.7606 (m-30) REVERT: l 77 ASP cc_start: 0.7942 (m-30) cc_final: 0.7722 (m-30) outliers start: 2 outliers final: 1 residues processed: 1062 average time/residue: 1.4087 time to fit residues: 1996.5867 Evaluate side-chains 586 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 585 time to evaluate : 6.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 186 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 866 optimal weight: 3.9990 chunk 777 optimal weight: 4.9990 chunk 431 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 524 optimal weight: 2.9990 chunk 415 optimal weight: 0.6980 chunk 804 optimal weight: 0.6980 chunk 311 optimal weight: 0.0870 chunk 488 optimal weight: 9.9990 chunk 598 optimal weight: 0.8980 chunk 931 optimal weight: 7.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN B 18 ASN B 30 GLN C 28 GLN C 130 ASN C 134 ASN D 231 ASN E 30 GLN F 134 ASN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 GLN H 45 ASN H 123 GLN I 28 GLN I 34 ASN I 45 ASN I 54 ASN I 252 GLN J 23 ASN J 28 GLN J 263 GLN L 263 GLN M 28 GLN M 54 ASN N 45 ASN N 54 ASN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 20 ASN O 23 ASN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 GLN O 151 ASN O 251 GLN P 111 ASN P 123 GLN ** P 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 252 GLN Q 256 GLN R 106 ASN R 248 GLN R 262 ASN S 7 ASN ** S 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 GLN T 30 GLN T 54 ASN ** U 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 151 ASN U 263 GLN V 123 GLN V 231 ASN ** W 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 134 ASN W 151 ASN W 263 GLN X 28 GLN X 73 GLN Y 7 ASN Y 123 GLN Z 63 ASN a 4 ASN ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 7 ASN b 130 ASN c 18 ASN c 28 GLN c 30 GLN c 123 GLN d 18 ASN d 28 GLN d 30 GLN d 130 ASN d 263 GLN e 18 ASN e 28 GLN f 73 GLN g 30 GLN g 263 GLN ** h 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 130 ASN i 195 GLN i 199 ASN j 256 GLN l 18 ASN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.119864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103510 restraints weight = 109864.492| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.45 r_work: 0.3344 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 73796 Z= 0.172 Angle : 0.480 11.437 99864 Z= 0.271 Chirality : 0.033 0.270 12844 Planarity : 0.003 0.033 12768 Dihedral : 3.934 37.941 10339 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 2.03 % Allowed : 6.92 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.08), residues: 10184 helix: 3.06 (0.05), residues: 7334 sheet: -3.53 (0.18), residues: 380 loop : 1.67 (0.14), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 49 HIS 0.003 0.001 HIS h 214 PHE 0.027 0.002 PHE X 117 ARG 0.007 0.001 ARG a 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 685 time to evaluate : 6.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: G 262 ASN cc_start: 0.6067 (m110) cc_final: 0.5861 (m110) REVERT: I 252 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8250 (mt0) REVERT: J 84 ASP cc_start: 0.8231 (m-30) cc_final: 0.7895 (m-30) REVERT: K 62 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8155 (mtt) REVERT: L 56 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8344 (m) REVERT: N 25 GLU cc_start: 0.8715 (tt0) cc_final: 0.8478 (tt0) REVERT: N 208 SER cc_start: 0.8052 (t) cc_final: 0.7788 (p) REVERT: O 151 ASN cc_start: 0.8107 (t0) cc_final: 0.7504 (t0) REVERT: O 258 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8292 (tt) REVERT: P 77 ASP cc_start: 0.7896 (m-30) cc_final: 0.7608 (m-30) REVERT: P 130 ASN cc_start: 0.7692 (m110) cc_final: 0.7474 (m110) REVERT: Q 126 LYS cc_start: 0.7543 (ttmt) cc_final: 0.6847 (tttt) REVERT: Q 189 THR cc_start: 0.7655 (p) cc_final: 0.7391 (p) REVERT: R 240 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7112 (mm-30) REVERT: S 25 GLU cc_start: 0.7981 (mp0) cc_final: 0.7713 (mm-30) REVERT: S 62 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7704 (mtp) REVERT: T 77 ASP cc_start: 0.7241 (m-30) cc_final: 0.6987 (m-30) REVERT: T 151 ASN cc_start: 0.8441 (t0) cc_final: 0.8136 (t0) REVERT: T 245 GLN cc_start: 0.7477 (mp10) cc_final: 0.7170 (mp10) REVERT: U 62 MET cc_start: 0.7524 (mmt) cc_final: 0.7293 (mmm) REVERT: U 101 SER cc_start: 0.7722 (t) cc_final: 0.7428 (m) REVERT: V 25 GLU cc_start: 0.7743 (tp30) cc_final: 0.7517 (tp30) REVERT: V 130 ASN cc_start: 0.7329 (m110) cc_final: 0.6907 (m110) REVERT: W 134 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.8010 (t0) REVERT: X 30 GLN cc_start: 0.7770 (mt0) cc_final: 0.7353 (tm-30) REVERT: X 164 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8068 (mp) REVERT: Y 263 GLN cc_start: 0.7424 (mt0) cc_final: 0.7120 (tp40) REVERT: Y 268 ILE cc_start: 0.8736 (pt) cc_final: 0.8458 (pt) REVERT: a 16 LEU cc_start: 0.7656 (mm) cc_final: 0.7423 (mm) REVERT: a 186 MET cc_start: 0.6596 (tpt) cc_final: 0.6340 (tpt) REVERT: a 226 ASP cc_start: 0.8332 (m-30) cc_final: 0.8038 (m-30) REVERT: b 29 VAL cc_start: 0.8405 (t) cc_final: 0.8200 (p) REVERT: b 171 LEU cc_start: 0.8247 (tp) cc_final: 0.8045 (mt) REVERT: f 26 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8439 (tt) REVERT: h 88 ASP cc_start: 0.8513 (m-30) cc_final: 0.8254 (m-30) REVERT: i 252 GLN cc_start: 0.8630 (mm110) cc_final: 0.8406 (mm-40) REVERT: k 8 THR cc_start: 0.8661 (t) cc_final: 0.8458 (m) REVERT: l 256 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7164 (tt0) outliers start: 162 outliers final: 49 residues processed: 804 average time/residue: 1.2549 time to fit residues: 1393.2349 Evaluate side-chains 616 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 557 time to evaluate : 6.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 252 GLN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 134 ASN Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 164 LEU Chi-restraints excluded: chain X residue 226 ASP Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 252 GLN Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 35 THR Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain j residue 84 ASP Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 256 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 650 optimal weight: 7.9990 chunk 756 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 412 optimal weight: 6.9990 chunk 588 optimal weight: 0.9990 chunk 921 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 604 optimal weight: 1.9990 chunk 274 optimal weight: 9.9990 chunk 287 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 262 ASN B 28 GLN B 34 ASN C 30 GLN D 18 ASN D 195 GLN E 30 GLN F 4 ASN F 20 ASN G 20 ASN ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN I 28 GLN I 34 ASN I 55 GLN I 252 GLN I 262 ASN J 30 GLN J 262 ASN K 18 ASN K 130 ASN L 28 GLN L 263 GLN M 28 GLN ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN O 18 ASN O 231 ASN P 30 GLN P 31 GLN P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 251 GLN Q 23 ASN Q 30 GLN Q 199 ASN R 263 GLN S 45 ASN S 73 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN U 248 GLN U 263 GLN V 30 GLN V 45 ASN V 55 GLN V 123 GLN ** W 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN W 134 ASN W 263 GLN Z 18 ASN Z 31 GLN ** a 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 GLN c 7 ASN c 23 ASN c 28 GLN c 63 ASN e 45 ASN ** e 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 130 ASN g 18 ASN h 34 ASN h 256 GLN i 262 ASN j 30 GLN k 18 ASN k 130 ASN l 130 ASN Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095850 restraints weight = 115218.486| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.51 r_work: 0.3254 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 73796 Z= 0.419 Angle : 0.610 12.596 99864 Z= 0.335 Chirality : 0.040 0.274 12844 Planarity : 0.003 0.044 12768 Dihedral : 4.132 20.640 10336 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.02 % Allowed : 8.30 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.91 (0.08), residues: 10184 helix: 3.41 (0.05), residues: 7182 sheet: -3.62 (0.15), residues: 456 loop : 1.43 (0.14), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 49 HIS 0.006 0.002 HIS l 214 PHE 0.029 0.002 PHE U 148 ARG 0.007 0.001 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 560 time to evaluate : 6.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.8639 (mt0) cc_final: 0.8357 (mt0) REVERT: D 195 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: H 62 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7046 (mtt) REVERT: H 272 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7622 (t80) REVERT: J 71 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8063 (ptp90) REVERT: K 62 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8480 (mtt) REVERT: L 31 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7640 (mp-120) REVERT: M 212 ASP cc_start: 0.7288 (t70) cc_final: 0.6859 (t0) REVERT: M 268 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7124 (pt) REVERT: O 151 ASN cc_start: 0.8191 (t0) cc_final: 0.7694 (t0) REVERT: O 258 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8451 (tt) REVERT: P 77 ASP cc_start: 0.7964 (m-30) cc_final: 0.7709 (m-30) REVERT: P 130 ASN cc_start: 0.7960 (m110) cc_final: 0.7688 (m110) REVERT: R 28 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8139 (mm-40) REVERT: R 62 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8512 (mtt) REVERT: R 251 GLN cc_start: 0.8401 (tt0) cc_final: 0.8085 (tt0) REVERT: S 45 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8191 (t0) REVERT: S 62 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7955 (mtp) REVERT: S 240 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: T 77 ASP cc_start: 0.7446 (m-30) cc_final: 0.7231 (m-30) REVERT: T 151 ASN cc_start: 0.8618 (t0) cc_final: 0.8305 (t0) REVERT: V 130 ASN cc_start: 0.7763 (m110) cc_final: 0.7274 (m110) REVERT: V 186 MET cc_start: 0.8495 (mmt) cc_final: 0.7987 (mmt) REVERT: X 30 GLN cc_start: 0.8052 (mt0) cc_final: 0.7636 (tm130) REVERT: X 164 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8259 (mp) REVERT: Y 134 ASN cc_start: 0.8330 (t0) cc_final: 0.7857 (t0) REVERT: Y 268 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8577 (pt) REVERT: a 70 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6503 (tt0) REVERT: a 246 SER cc_start: 0.8561 (m) cc_final: 0.8148 (p) REVERT: b 30 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: e 110 PHE cc_start: 0.6550 (t80) cc_final: 0.6275 (t80) REVERT: f 26 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8469 (tt) REVERT: h 88 ASP cc_start: 0.8604 (m-30) cc_final: 0.8352 (m-30) REVERT: i 26 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8761 (tt) REVERT: k 251 GLN cc_start: 0.9300 (tt0) cc_final: 0.9088 (tt0) REVERT: l 256 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7239 (tt0) outliers start: 241 outliers final: 108 residues processed: 739 average time/residue: 1.3176 time to fit residues: 1325.6727 Evaluate side-chains 630 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 502 time to evaluate : 6.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 270 SER Chi-restraints excluded: chain H residue 272 PHE Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 71 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 268 ILE Chi-restraints excluded: chain N residue 138 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 28 GLN Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 88 ASP Chi-restraints excluded: chain R residue 267 SER Chi-restraints excluded: chain S residue 45 ASN Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 18 ASN Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 174 THR Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 164 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 268 ILE Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain Z residue 268 ILE Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 68 SER Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 30 GLN Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 126 LYS Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 84 ASP Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 125 THR Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 95 GLU Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 95 GLU Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain j residue 268 ILE Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain k residue 268 ILE Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 256 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 514 optimal weight: 2.9990 chunk 919 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 800 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 598 optimal weight: 3.9990 chunk 858 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 930 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN E 30 GLN G 134 ASN H 123 GLN I 28 GLN I 34 ASN I 252 GLN L 263 GLN M 28 GLN N 31 GLN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 ASN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 ASN P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 45 ASN S 73 GLN ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 134 ASN W 263 GLN ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 GLN c 28 GLN ** e 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 263 GLN h 34 ASN j 55 GLN j 263 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.098152 restraints weight = 111333.063| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.44 r_work: 0.3268 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 73796 Z= 0.186 Angle : 0.448 9.631 99864 Z= 0.256 Chirality : 0.033 0.219 12844 Planarity : 0.002 0.026 12768 Dihedral : 3.790 17.243 10336 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.71 % Allowed : 9.79 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.45 (0.08), residues: 10184 helix: 3.83 (0.05), residues: 7334 sheet: -3.02 (0.17), residues: 380 loop : 1.12 (0.14), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 49 HIS 0.004 0.001 HIS h 214 PHE 0.027 0.001 PHE X 117 ARG 0.004 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 587 time to evaluate : 6.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8273 (m110) REVERT: H 26 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8468 (tt) REVERT: H 272 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7880 (t80) REVERT: I 31 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7697 (mm-40) REVERT: I 252 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: I 268 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7912 (mp) REVERT: J 84 ASP cc_start: 0.8350 (m-30) cc_final: 0.7979 (m-30) REVERT: M 118 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6222 (m-30) REVERT: O 151 ASN cc_start: 0.8103 (t0) cc_final: 0.7606 (t0) REVERT: O 258 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8364 (tt) REVERT: P 77 ASP cc_start: 0.7817 (m-30) cc_final: 0.7552 (m-30) REVERT: P 130 ASN cc_start: 0.7844 (m110) cc_final: 0.7576 (m110) REVERT: R 28 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8044 (mm-40) REVERT: R 62 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: S 32 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7471 (ttm170) REVERT: S 62 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8058 (mtp) REVERT: T 77 ASP cc_start: 0.7313 (m-30) cc_final: 0.7015 (m-30) REVERT: T 151 ASN cc_start: 0.8544 (t0) cc_final: 0.8245 (t0) REVERT: U 259 SER cc_start: 0.8949 (t) cc_final: 0.8488 (m) REVERT: V 130 ASN cc_start: 0.7410 (m110) cc_final: 0.6853 (m110) REVERT: V 186 MET cc_start: 0.8420 (mmt) cc_final: 0.7983 (mmt) REVERT: X 30 GLN cc_start: 0.7914 (mt0) cc_final: 0.7412 (tm130) REVERT: X 84 ASP cc_start: 0.8388 (p0) cc_final: 0.7996 (m-30) REVERT: Y 212 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: Y 268 ILE cc_start: 0.8775 (pt) cc_final: 0.8503 (pt) REVERT: a 13 LEU cc_start: 0.6986 (mt) cc_final: 0.6406 (mt) REVERT: a 16 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7658 (mm) REVERT: a 226 ASP cc_start: 0.8349 (m-30) cc_final: 0.8048 (m-30) REVERT: b 126 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8396 (tttp) REVERT: b 184 LYS cc_start: 0.5914 (tppt) cc_final: 0.5469 (tppt) REVERT: f 26 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8561 (tt) REVERT: h 88 ASP cc_start: 0.8547 (m-30) cc_final: 0.8273 (m-30) REVERT: h 243 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8242 (ttpt) REVERT: h 262 ASN cc_start: 0.7536 (m-40) cc_final: 0.7236 (m110) REVERT: i 252 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8454 (mm-40) REVERT: k 62 MET cc_start: 0.8971 (mmt) cc_final: 0.8751 (mtp) REVERT: k 251 GLN cc_start: 0.9283 (tt0) cc_final: 0.9036 (tt0) outliers start: 216 outliers final: 90 residues processed: 758 average time/residue: 1.2566 time to fit residues: 1311.1051 Evaluate side-chains 626 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 520 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 272 PHE Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 252 GLN Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain K residue 117 PHE Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 118 ASP Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 269 LEU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 28 GLN Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 267 SER Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 232 LEU Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 212 ASP Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain Z residue 268 ILE Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 84 ASP Chi-restraints excluded: chain a residue 92 LYS Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 126 LYS Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 71 ARG Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 LYS Chi-restraints excluded: chain e residue 215 LEU Chi-restraints excluded: chain e residue 263 GLN Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 116 ASP Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 243 LYS Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 729 optimal weight: 8.9990 chunk 858 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 300 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 469 optimal weight: 0.6980 chunk 481 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 372 optimal weight: 0.9990 chunk 161 optimal weight: 0.4980 chunk 395 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 ASN C 30 GLN D 130 ASN E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN I 28 GLN I 34 ASN K 263 GLN L 263 GLN M 28 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 263 GLN ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN e 263 GLN g 18 ASN h 34 ASN h 256 GLN i 262 ASN j 263 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101243 restraints weight = 110657.467| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.52 r_work: 0.3307 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 73796 Z= 0.146 Angle : 0.414 9.744 99864 Z= 0.238 Chirality : 0.031 0.194 12844 Planarity : 0.002 0.026 12768 Dihedral : 3.614 21.376 10336 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.26 % Allowed : 11.03 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.08), residues: 10184 helix: 4.11 (0.05), residues: 7334 sheet: -2.70 (0.18), residues: 380 loop : 1.17 (0.14), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 49 HIS 0.003 0.001 HIS h 214 PHE 0.027 0.001 PHE X 117 ARG 0.006 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 638 time to evaluate : 6.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8255 (m110) REVERT: C 140 ASP cc_start: 0.8112 (p0) cc_final: 0.7909 (p0) REVERT: D 195 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6194 (tm-30) REVERT: F 3 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6467 (mt) REVERT: G 272 PHE cc_start: 0.5837 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: H 272 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7774 (t80) REVERT: I 32 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.8086 (ttp-110) REVERT: J 84 ASP cc_start: 0.8230 (m-30) cc_final: 0.7863 (m-30) REVERT: L 56 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8307 (m) REVERT: N 208 SER cc_start: 0.8121 (OUTLIER) cc_final: 0.7517 (p) REVERT: O 151 ASN cc_start: 0.8114 (t0) cc_final: 0.7575 (t0) REVERT: O 258 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8197 (tt) REVERT: P 77 ASP cc_start: 0.7840 (m-30) cc_final: 0.7569 (m-30) REVERT: P 130 ASN cc_start: 0.7755 (m110) cc_final: 0.7522 (m110) REVERT: Q 95 GLU cc_start: 0.4988 (OUTLIER) cc_final: 0.3700 (mp0) REVERT: Q 126 LYS cc_start: 0.7626 (ttmt) cc_final: 0.6728 (tttt) REVERT: R 28 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8001 (mm-40) REVERT: R 62 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8277 (mtt) REVERT: R 95 GLU cc_start: 0.8844 (tt0) cc_final: 0.8563 (tt0) REVERT: R 191 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: S 32 ARG cc_start: 0.7797 (ttp-110) cc_final: 0.7500 (ttp-170) REVERT: S 240 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: T 151 ASN cc_start: 0.8545 (t0) cc_final: 0.8228 (t0) REVERT: V 130 ASN cc_start: 0.7178 (m110) cc_final: 0.6570 (m110) REVERT: V 269 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7374 (tp) REVERT: X 30 GLN cc_start: 0.7753 (mt0) cc_final: 0.7264 (tm-30) REVERT: X 84 ASP cc_start: 0.8441 (p0) cc_final: 0.7927 (m-30) REVERT: Y 212 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: Y 263 GLN cc_start: 0.7346 (mt0) cc_final: 0.7050 (tp40) REVERT: Y 268 ILE cc_start: 0.8694 (pt) cc_final: 0.8428 (pt) REVERT: a 94 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6612 (tmmt) REVERT: f 26 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8497 (tt) REVERT: f 31 GLN cc_start: 0.8304 (mt0) cc_final: 0.8096 (mt0) REVERT: h 88 ASP cc_start: 0.8547 (m-30) cc_final: 0.8260 (m-30) REVERT: h 243 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8078 (ttpt) REVERT: h 262 ASN cc_start: 0.7400 (m-40) cc_final: 0.7086 (m110) REVERT: h 263 GLN cc_start: 0.7612 (mt0) cc_final: 0.7359 (mt0) REVERT: i 174 THR cc_start: 0.8436 (m) cc_final: 0.8231 (t) REVERT: i 252 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8411 (mm-40) REVERT: k 251 GLN cc_start: 0.9274 (tt0) cc_final: 0.9067 (tt0) outliers start: 180 outliers final: 73 residues processed: 777 average time/residue: 1.2688 time to fit residues: 1360.3239 Evaluate side-chains 629 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 538 time to evaluate : 6.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 272 PHE Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 270 SER Chi-restraints excluded: chain H residue 272 PHE Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 117 PHE Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 267 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 5 SER Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 28 GLN Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain R residue 267 SER Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 226 ASP Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 212 ASP Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 84 ASP Chi-restraints excluded: chain a residue 92 LYS Chi-restraints excluded: chain a residue 94 LYS Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 95 GLU Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain e residue 215 LEU Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 243 LYS Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 74 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 623 optimal weight: 0.7980 chunk 357 optimal weight: 10.0000 chunk 532 optimal weight: 0.6980 chunk 493 optimal weight: 8.9990 chunk 824 optimal weight: 0.9990 chunk 797 optimal weight: 0.0040 chunk 952 optimal weight: 1.9990 chunk 785 optimal weight: 4.9990 chunk 520 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 GLN F 4 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN H 20 ASN H 30 GLN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN I 28 GLN I 34 ASN I 252 GLN K 263 GLN M 28 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 ASN P 111 ASN P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 262 ASN R 251 GLN ** R 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN Z 31 GLN Z 199 ASN ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 130 ASN b 195 GLN c 28 GLN e 262 ASN f 231 ASN h 256 GLN j 263 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103608 restraints weight = 110347.275| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.44 r_work: 0.3353 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 73796 Z= 0.137 Angle : 0.406 11.526 99864 Z= 0.232 Chirality : 0.031 0.260 12844 Planarity : 0.002 0.028 12768 Dihedral : 3.507 14.921 10336 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.99 % Allowed : 11.87 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.99 (0.08), residues: 10184 helix: 4.23 (0.05), residues: 7334 sheet: -2.38 (0.18), residues: 380 loop : 1.21 (0.14), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 49 HIS 0.002 0.001 HIS h 214 PHE 0.025 0.001 PHE X 117 ARG 0.006 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 649 time to evaluate : 6.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 195 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.6262 (tm-30) REVERT: E 191 ASP cc_start: 0.8410 (m-30) cc_final: 0.8146 (m-30) REVERT: F 3 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6499 (mt) REVERT: G 272 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5564 (m-80) REVERT: H 272 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7816 (t80) REVERT: I 32 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8130 (ttp-110) REVERT: I 252 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: J 84 ASP cc_start: 0.8104 (m-30) cc_final: 0.7831 (m-30) REVERT: L 56 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8260 (m) REVERT: N 208 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7520 (p) REVERT: O 151 ASN cc_start: 0.8106 (t0) cc_final: 0.7613 (t0) REVERT: O 258 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8242 (tt) REVERT: P 77 ASP cc_start: 0.7820 (m-30) cc_final: 0.7524 (m-30) REVERT: Q 95 GLU cc_start: 0.5340 (OUTLIER) cc_final: 0.3998 (mp0) REVERT: Q 126 LYS cc_start: 0.7692 (ttmt) cc_final: 0.6812 (tttt) REVERT: R 95 GLU cc_start: 0.8830 (tt0) cc_final: 0.8554 (tt0) REVERT: R 116 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6333 (t0) REVERT: R 191 ASP cc_start: 0.7339 (t0) cc_final: 0.6799 (m-30) REVERT: S 32 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7543 (ttp-170) REVERT: S 240 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: T 151 ASN cc_start: 0.8583 (t0) cc_final: 0.8281 (t0) REVERT: T 245 GLN cc_start: 0.7432 (mp10) cc_final: 0.7117 (mp10) REVERT: T 263 GLN cc_start: 0.8132 (mt0) cc_final: 0.7866 (mt0) REVERT: U 101 SER cc_start: 0.7626 (t) cc_final: 0.7206 (m) REVERT: X 30 GLN cc_start: 0.7760 (mt0) cc_final: 0.7347 (tm-30) REVERT: X 84 ASP cc_start: 0.8448 (p0) cc_final: 0.7909 (m-30) REVERT: X 147 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7919 (m) REVERT: Y 26 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8290 (tp) REVERT: Y 212 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: Y 268 ILE cc_start: 0.8681 (pt) cc_final: 0.8394 (pt) REVERT: a 26 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8827 (tp) REVERT: b 184 LYS cc_start: 0.6389 (tppt) cc_final: 0.5985 (tttt) REVERT: c 126 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7676 (tttp) REVERT: f 26 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8556 (tt) REVERT: h 88 ASP cc_start: 0.8550 (m-30) cc_final: 0.8288 (m-30) REVERT: h 263 GLN cc_start: 0.7597 (mt0) cc_final: 0.7233 (tt0) REVERT: i 252 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8478 (mm-40) REVERT: j 262 ASN cc_start: 0.8311 (m-40) cc_final: 0.8110 (m110) REVERT: k 251 GLN cc_start: 0.9292 (tt0) cc_final: 0.9057 (tt0) REVERT: l 84 ASP cc_start: 0.7191 (m-30) cc_final: 0.6807 (m-30) outliers start: 159 outliers final: 72 residues processed: 774 average time/residue: 1.2471 time to fit residues: 1340.9603 Evaluate side-chains 659 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 570 time to evaluate : 6.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 272 PHE Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 272 PHE Chi-restraints excluded: chain I residue 252 GLN Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 31 GLN Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 212 ASP Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain c residue 126 LYS Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 98 LEU Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain e residue 215 LEU Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 411 optimal weight: 1.9990 chunk 39 optimal weight: 0.0040 chunk 618 optimal weight: 1.9990 chunk 562 optimal weight: 5.9990 chunk 1008 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 1018 optimal weight: 2.9990 chunk 900 optimal weight: 1.9990 chunk 468 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 ASN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 GLN I 28 GLN I 34 ASN I 252 GLN J 28 GLN K 263 GLN M 28 GLN ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 262 ASN U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN X 214 HIS Z 123 GLN ** a 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 28 GLN e 262 ASN h 256 GLN ** i 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 231 ASN j 256 GLN j 263 GLN l 256 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.117808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101510 restraints weight = 110636.262| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.44 r_work: 0.3318 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 73796 Z= 0.163 Angle : 0.430 12.276 99864 Z= 0.243 Chirality : 0.032 0.361 12844 Planarity : 0.002 0.029 12768 Dihedral : 3.525 15.220 10336 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.04 % Allowed : 12.31 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.08), residues: 10184 helix: 4.18 (0.05), residues: 7334 sheet: -2.66 (0.17), residues: 456 loop : 1.26 (0.15), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 49 HIS 0.003 0.001 HIS h 214 PHE 0.027 0.001 PHE X 117 ARG 0.005 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 600 time to evaluate : 6.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 191 ASP cc_start: 0.8383 (m-30) cc_final: 0.8121 (m-30) REVERT: F 3 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6331 (mt) REVERT: G 191 ASP cc_start: 0.8136 (m-30) cc_final: 0.7911 (m-30) REVERT: G 272 PHE cc_start: 0.5959 (OUTLIER) cc_final: 0.5650 (m-80) REVERT: H 272 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7817 (t80) REVERT: I 252 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: J 84 ASP cc_start: 0.8145 (m-30) cc_final: 0.7870 (m-30) REVERT: K 232 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8036 (mp) REVERT: L 56 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8322 (m) REVERT: N 208 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7700 (p) REVERT: O 151 ASN cc_start: 0.8125 (t0) cc_final: 0.7596 (t0) REVERT: O 258 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8346 (tt) REVERT: P 77 ASP cc_start: 0.7864 (m-30) cc_final: 0.7582 (m-30) REVERT: Q 95 GLU cc_start: 0.5284 (OUTLIER) cc_final: 0.3882 (mp0) REVERT: R 95 GLU cc_start: 0.8760 (tt0) cc_final: 0.8559 (tt0) REVERT: R 191 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: S 32 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7595 (ttp-170) REVERT: S 240 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: T 151 ASN cc_start: 0.8599 (t0) cc_final: 0.8306 (t0) REVERT: T 263 GLN cc_start: 0.8214 (mt0) cc_final: 0.7914 (mt0) REVERT: U 62 MET cc_start: 0.7758 (mmp) cc_final: 0.7513 (mmm) REVERT: U 101 SER cc_start: 0.7583 (t) cc_final: 0.7148 (m) REVERT: X 30 GLN cc_start: 0.7923 (mt0) cc_final: 0.7417 (tm-30) REVERT: X 84 ASP cc_start: 0.8479 (p0) cc_final: 0.7926 (m-30) REVERT: Y 26 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8224 (tp) REVERT: Y 212 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: Y 263 GLN cc_start: 0.7748 (tp40) cc_final: 0.7300 (tt0) REVERT: Y 268 ILE cc_start: 0.8642 (pt) cc_final: 0.8390 (pt) REVERT: a 26 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8798 (tp) REVERT: a 116 ASP cc_start: 0.6588 (m-30) cc_final: 0.6111 (m-30) REVERT: e 263 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: f 26 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8563 (tt) REVERT: h 88 ASP cc_start: 0.8579 (m-30) cc_final: 0.8308 (m-30) REVERT: h 263 GLN cc_start: 0.7696 (mt0) cc_final: 0.7307 (tt0) REVERT: k 251 GLN cc_start: 0.9309 (tt0) cc_final: 0.9071 (tt0) REVERT: k 256 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: l 84 ASP cc_start: 0.7242 (m-30) cc_final: 0.6817 (m-30) outliers start: 163 outliers final: 93 residues processed: 728 average time/residue: 1.2243 time to fit residues: 1244.8633 Evaluate side-chains 665 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 555 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 272 PHE Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 272 PHE Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 252 GLN Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 253 LEU Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain R residue 267 SER Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 226 ASP Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Y residue 212 ASP Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 84 ASP Chi-restraints excluded: chain a residue 92 LYS Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 84 ASP Chi-restraints excluded: chain c residue 84 ASP Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 98 LEU Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain e residue 263 GLN Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain f residue 268 ILE Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain j residue 268 ILE Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 322 optimal weight: 10.0000 chunk 909 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 601 optimal weight: 3.9990 chunk 961 optimal weight: 1.9990 chunk 770 optimal weight: 5.9990 chunk 742 optimal weight: 8.9990 chunk 626 optimal weight: 6.9990 chunk 803 optimal weight: 10.0000 chunk 467 optimal weight: 0.8980 chunk 423 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 GLN E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN H 123 GLN H 256 GLN I 28 GLN I 34 ASN I 252 GLN K 263 GLN M 28 GLN N 30 GLN N 31 GLN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 ASN S 31 GLN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN a 111 ASN b 130 ASN c 28 GLN c 263 GLN g 18 ASN h 34 ASN h 256 GLN ** i 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 263 GLN l 256 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.095855 restraints weight = 111738.514| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.44 r_work: 0.3237 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 73796 Z= 0.243 Angle : 0.495 12.420 99864 Z= 0.276 Chirality : 0.035 0.355 12844 Planarity : 0.002 0.028 12768 Dihedral : 3.734 17.712 10336 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.27 % Allowed : 12.26 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.08), residues: 10184 helix: 3.95 (0.05), residues: 7334 sheet: -2.68 (0.17), residues: 456 loop : 1.10 (0.14), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 49 HIS 0.004 0.002 HIS l 214 PHE 0.033 0.002 PHE X 117 ARG 0.003 0.000 ARG H 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 557 time to evaluate : 6.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: D 86 ILE cc_start: 0.8110 (mm) cc_final: 0.7841 (mt) REVERT: E 191 ASP cc_start: 0.8393 (m-30) cc_final: 0.8084 (m-30) REVERT: F 3 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6480 (mt) REVERT: G 272 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5849 (m-80) REVERT: H 114 LYS cc_start: 0.6955 (ptmm) cc_final: 0.6690 (mtpp) REVERT: H 272 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7835 (t80) REVERT: I 32 ARG cc_start: 0.8454 (ttp-110) cc_final: 0.8228 (ttp-170) REVERT: I 268 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.8002 (mp) REVERT: J 84 ASP cc_start: 0.8358 (m-30) cc_final: 0.7992 (m-30) REVERT: K 232 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8238 (mp) REVERT: L 56 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8327 (m) REVERT: M 16 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7048 (mm) REVERT: O 151 ASN cc_start: 0.8178 (t0) cc_final: 0.7630 (t0) REVERT: O 253 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8354 (tt) REVERT: O 258 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8413 (tt) REVERT: P 77 ASP cc_start: 0.7889 (m-30) cc_final: 0.7620 (m-30) REVERT: Q 95 GLU cc_start: 0.5368 (OUTLIER) cc_final: 0.3994 (mp0) REVERT: S 32 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7578 (ttp-170) REVERT: S 240 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: T 151 ASN cc_start: 0.8645 (t0) cc_final: 0.8342 (t0) REVERT: U 174 THR cc_start: 0.8154 (t) cc_final: 0.7931 (m) REVERT: X 30 GLN cc_start: 0.7886 (mt0) cc_final: 0.7512 (tm-30) REVERT: X 34 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7748 (p0) REVERT: X 84 ASP cc_start: 0.8517 (p0) cc_final: 0.8032 (m-30) REVERT: Y 26 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8168 (tp) REVERT: Y 134 ASN cc_start: 0.8213 (t0) cc_final: 0.7998 (t0) REVERT: Y 263 GLN cc_start: 0.7773 (tp40) cc_final: 0.7332 (tt0) REVERT: a 26 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8782 (tp) REVERT: a 55 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.5996 (mp10) REVERT: a 116 ASP cc_start: 0.6793 (m-30) cc_final: 0.6357 (m-30) REVERT: b 184 LYS cc_start: 0.6563 (tppt) cc_final: 0.6068 (tppt) REVERT: e 114 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7419 (mmmt) REVERT: e 263 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: f 26 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8547 (tt) REVERT: h 263 GLN cc_start: 0.7779 (mt0) cc_final: 0.7544 (mt0) REVERT: k 256 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8184 (tt0) outliers start: 181 outliers final: 99 residues processed: 693 average time/residue: 1.2660 time to fit residues: 1213.0842 Evaluate side-chains 638 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 519 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 272 PHE Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 270 SER Chi-restraints excluded: chain H residue 272 PHE Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 149 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 28 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 267 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 267 SER Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 92 LYS Chi-restraints excluded: chain a residue 179 THR Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 123 GLN Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 5 SER Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain e residue 215 LEU Chi-restraints excluded: chain e residue 263 GLN Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain f residue 268 ILE Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 268 ILE Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 155 SER Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 472 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 411 optimal weight: 0.9980 chunk 570 optimal weight: 0.5980 chunk 916 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 327 optimal weight: 0.7980 chunk 804 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 256 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN H 123 GLN I 28 GLN I 34 ASN J 28 GLN K 130 ASN K 263 GLN M 28 GLN ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN W 263 GLN X 34 ASN c 28 GLN h 34 ASN h 256 GLN ** i 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 263 GLN l 256 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.117089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100863 restraints weight = 110652.727| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.44 r_work: 0.3314 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 73796 Z= 0.151 Angle : 0.432 12.684 99864 Z= 0.245 Chirality : 0.032 0.324 12844 Planarity : 0.002 0.019 12768 Dihedral : 3.556 16.083 10336 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.73 % Allowed : 13.02 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.86 (0.08), residues: 10184 helix: 4.18 (0.05), residues: 7334 sheet: -2.54 (0.17), residues: 456 loop : 1.17 (0.15), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 49 HIS 0.003 0.001 HIS h 214 PHE 0.027 0.001 PHE X 117 ARG 0.003 0.000 ARG H 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 566 time to evaluate : 6.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 195 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6124 (tm-30) REVERT: E 191 ASP cc_start: 0.8390 (m-30) cc_final: 0.8112 (m-30) REVERT: F 3 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6268 (mt) REVERT: G 272 PHE cc_start: 0.6065 (OUTLIER) cc_final: 0.5799 (m-80) REVERT: H 272 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7818 (t80) REVERT: I 114 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7947 (tttp) REVERT: J 84 ASP cc_start: 0.8214 (m-30) cc_final: 0.7936 (m-30) REVERT: L 56 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8308 (m) REVERT: M 16 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7089 (mm) REVERT: N 208 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7566 (p) REVERT: O 35 THR cc_start: 0.7926 (t) cc_final: 0.7658 (m) REVERT: O 151 ASN cc_start: 0.8155 (t0) cc_final: 0.7620 (t0) REVERT: P 77 ASP cc_start: 0.7833 (m-30) cc_final: 0.7565 (m-30) REVERT: Q 95 GLU cc_start: 0.5277 (OUTLIER) cc_final: 0.3938 (mp0) REVERT: Q 123 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6509 (mm-40) REVERT: Q 179 THR cc_start: 0.7480 (m) cc_final: 0.7110 (p) REVERT: R 191 ASP cc_start: 0.7474 (t0) cc_final: 0.6907 (m-30) REVERT: S 32 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7551 (ttm170) REVERT: S 240 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: T 151 ASN cc_start: 0.8620 (t0) cc_final: 0.8312 (t0) REVERT: T 245 GLN cc_start: 0.7424 (mp10) cc_final: 0.7134 (mp10) REVERT: T 263 GLN cc_start: 0.8217 (mt0) cc_final: 0.7943 (mt0) REVERT: U 31 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: U 62 MET cc_start: 0.7957 (mmt) cc_final: 0.7699 (mmm) REVERT: U 101 SER cc_start: 0.7671 (t) cc_final: 0.7224 (m) REVERT: X 30 GLN cc_start: 0.7926 (mt0) cc_final: 0.7445 (tm-30) REVERT: X 84 ASP cc_start: 0.8496 (p0) cc_final: 0.7899 (m-30) REVERT: X 132 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6363 (mppt) REVERT: X 147 SER cc_start: 0.8143 (OUTLIER) cc_final: 0.7935 (m) REVERT: Y 26 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8216 (tp) REVERT: Y 212 ASP cc_start: 0.8068 (m-30) cc_final: 0.7814 (m-30) REVERT: Y 263 GLN cc_start: 0.7776 (tp40) cc_final: 0.7213 (tt0) REVERT: Y 268 ILE cc_start: 0.8685 (pt) cc_final: 0.8406 (pt) REVERT: a 26 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8782 (tp) REVERT: a 116 ASP cc_start: 0.6525 (m-30) cc_final: 0.6166 (m-30) REVERT: e 263 GLN cc_start: 0.7856 (tp40) cc_final: 0.7404 (mm110) REVERT: f 26 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8571 (tt) REVERT: h 88 ASP cc_start: 0.8567 (m-30) cc_final: 0.8286 (m-30) REVERT: h 262 ASN cc_start: 0.7756 (m-40) cc_final: 0.7546 (m110) REVERT: h 263 GLN cc_start: 0.7701 (mt0) cc_final: 0.7290 (tt0) REVERT: k 256 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8196 (tt0) outliers start: 138 outliers final: 79 residues processed: 675 average time/residue: 1.2463 time to fit residues: 1177.0056 Evaluate side-chains 634 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 538 time to evaluate : 6.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 195 GLN Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 272 PHE Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 272 PHE Chi-restraints excluded: chain I residue 114 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 28 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 134 ASN Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 267 SER Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 268 ILE Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 132 LYS Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 84 ASP Chi-restraints excluded: chain a residue 92 LYS Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 98 LEU Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain f residue 268 ILE Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 582 optimal weight: 9.9990 chunk 443 optimal weight: 3.9990 chunk 436 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 840 optimal weight: 5.9990 chunk 874 optimal weight: 3.9990 chunk 855 optimal weight: 2.9990 chunk 417 optimal weight: 0.9990 chunk 696 optimal weight: 7.9990 chunk 543 optimal weight: 0.1980 chunk 839 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN H 30 GLN H 123 GLN I 28 GLN I 34 ASN J 28 GLN K 263 GLN M 28 GLN N 28 GLN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 245 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN ** V 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN b 130 ASN c 28 GLN e 34 ASN h 34 ASN h 256 GLN ** i 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 263 GLN k 4 ASN l 256 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.113756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097210 restraints weight = 111019.714| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.52 r_work: 0.3246 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 73796 Z= 0.222 Angle : 0.488 12.778 99864 Z= 0.273 Chirality : 0.034 0.323 12844 Planarity : 0.002 0.025 12768 Dihedral : 3.669 16.407 10336 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.70 % Allowed : 13.20 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.08), residues: 10184 helix: 3.99 (0.05), residues: 7334 sheet: -2.55 (0.17), residues: 456 loop : 1.08 (0.14), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 49 HIS 0.004 0.002 HIS l 214 PHE 0.028 0.002 PHE X 117 ARG 0.005 0.000 ARG I 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20368 Ramachandran restraints generated. 10184 Oldfield, 0 Emsley, 10184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 538 time to evaluate : 6.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 263 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: E 191 ASP cc_start: 0.8373 (m-30) cc_final: 0.8071 (m-30) REVERT: F 3 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6373 (mt) REVERT: G 272 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5810 (m-80) REVERT: H 272 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7796 (t80) REVERT: I 268 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.8001 (mp) REVERT: J 84 ASP cc_start: 0.8299 (m-30) cc_final: 0.7922 (m-30) REVERT: K 232 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8099 (mp) REVERT: L 56 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8294 (m) REVERT: M 16 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.7001 (mm) REVERT: O 151 ASN cc_start: 0.8186 (t0) cc_final: 0.7611 (t0) REVERT: O 253 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8259 (tt) REVERT: P 77 ASP cc_start: 0.7921 (m-30) cc_final: 0.7634 (m-30) REVERT: Q 95 GLU cc_start: 0.5294 (OUTLIER) cc_final: 0.3922 (mp0) REVERT: Q 123 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6401 (mm-40) REVERT: Q 179 THR cc_start: 0.7476 (m) cc_final: 0.7096 (p) REVERT: S 32 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7533 (ttp-170) REVERT: S 240 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: T 151 ASN cc_start: 0.8653 (t0) cc_final: 0.8355 (t0) REVERT: T 245 GLN cc_start: 0.7431 (mp10) cc_final: 0.7060 (mp10) REVERT: T 263 GLN cc_start: 0.8271 (mt0) cc_final: 0.7962 (mt0) REVERT: U 31 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7252 (tt0) REVERT: X 30 GLN cc_start: 0.7841 (mt0) cc_final: 0.7381 (tm-30) REVERT: X 84 ASP cc_start: 0.8527 (p0) cc_final: 0.8026 (m-30) REVERT: Y 26 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8125 (tp) REVERT: Y 134 ASN cc_start: 0.8204 (t0) cc_final: 0.7979 (t0) REVERT: Y 263 GLN cc_start: 0.7757 (tp40) cc_final: 0.7216 (tt0) REVERT: Y 268 ILE cc_start: 0.8707 (pt) cc_final: 0.8427 (pt) REVERT: a 26 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8680 (tp) REVERT: a 55 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.5969 (mp10) REVERT: e 263 GLN cc_start: 0.7938 (tp40) cc_final: 0.7589 (mp10) REVERT: f 26 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8496 (tt) REVERT: h 263 GLN cc_start: 0.7674 (mt0) cc_final: 0.7252 (tt0) REVERT: k 256 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8126 (tt0) outliers start: 136 outliers final: 90 residues processed: 649 average time/residue: 1.2688 time to fit residues: 1141.6948 Evaluate side-chains 623 residues out of total 7980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 516 time to evaluate : 6.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 256 GLN Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 272 PHE Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 272 PHE Chi-restraints excluded: chain I residue 38 LYS Chi-restraints excluded: chain I residue 129 SER Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 272 PHE Chi-restraints excluded: chain K residue 186 MET Chi-restraints excluded: chain K residue 208 SER Chi-restraints excluded: chain K residue 232 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 268 ILE Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 208 SER Chi-restraints excluded: chain N residue 272 PHE Chi-restraints excluded: chain O residue 149 LEU Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 6 ILE Chi-restraints excluded: chain R residue 267 SER Chi-restraints excluded: chain S residue 240 GLU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 89 LEU Chi-restraints excluded: chain U residue 194 LEU Chi-restraints excluded: chain U residue 268 ILE Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 256 GLN Chi-restraints excluded: chain V residue 268 ILE Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain X residue 34 ASN Chi-restraints excluded: chain X residue 147 SER Chi-restraints excluded: chain X residue 159 VAL Chi-restraints excluded: chain X residue 269 LEU Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 56 SER Chi-restraints excluded: chain Y residue 69 LEU Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain Z residue 147 SER Chi-restraints excluded: chain Z residue 213 THR Chi-restraints excluded: chain a residue 17 GLN Chi-restraints excluded: chain a residue 26 LEU Chi-restraints excluded: chain a residue 55 GLN Chi-restraints excluded: chain a residue 92 LYS Chi-restraints excluded: chain a residue 245 GLN Chi-restraints excluded: chain a residue 270 SER Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 268 ILE Chi-restraints excluded: chain d residue 152 SER Chi-restraints excluded: chain d residue 174 THR Chi-restraints excluded: chain e residue 98 LEU Chi-restraints excluded: chain e residue 165 THR Chi-restraints excluded: chain f residue 26 LEU Chi-restraints excluded: chain f residue 28 GLN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 172 THR Chi-restraints excluded: chain f residue 174 THR Chi-restraints excluded: chain f residue 176 SER Chi-restraints excluded: chain f residue 268 ILE Chi-restraints excluded: chain g residue 267 SER Chi-restraints excluded: chain h residue 10 SER Chi-restraints excluded: chain h residue 198 THR Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 268 ILE Chi-restraints excluded: chain k residue 256 GLN Chi-restraints excluded: chain l residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1026 random chunks: chunk 702 optimal weight: 10.0000 chunk 786 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 546 optimal weight: 4.9990 chunk 986 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 636 optimal weight: 10.0000 chunk 503 optimal weight: 10.0000 chunk 556 optimal weight: 0.6980 chunk 656 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN E 30 GLN F 30 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 ASN H 123 GLN I 34 ASN J 134 ASN K 130 ASN K 263 GLN L 151 ASN M 28 GLN ** N 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 GLN ** O 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 ASN P 123 GLN P 151 ASN ** P 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 134 ASN S 20 ASN S 73 GLN T 31 GLN ** U 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 GLN V 55 GLN V 123 GLN b 123 GLN b 130 ASN c 28 GLN h 34 ASN h 256 GLN ** i 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 263 GLN l 245 GLN l 256 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.109254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092718 restraints weight = 115389.260| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.59 r_work: 0.3193 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 73796 Z= 0.456 Angle : 0.633 16.174 99864 Z= 0.345 Chirality : 0.042 0.325 12844 Planarity : 0.003 0.042 12768 Dihedral : 4.076 20.743 10336 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.01 % Allowed : 12.97 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.08), residues: 10184 helix: 3.60 (0.05), residues: 7182 sheet: -2.73 (0.17), residues: 456 loop : 0.94 (0.14), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 49 HIS 0.007 0.002 HIS e 214 PHE 0.031 0.003 PHE X 117 ARG 0.008 0.001 ARG I 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35541.08 seconds wall clock time: 612 minutes 55.32 seconds (36775.32 seconds total)