Starting phenix.real_space_refine on Sat Mar 7 04:24:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xl0_22231/03_2026/6xl0_22231.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xl0_22231/03_2026/6xl0_22231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xl0_22231/03_2026/6xl0_22231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xl0_22231/03_2026/6xl0_22231.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xl0_22231/03_2026/6xl0_22231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xl0_22231/03_2026/6xl0_22231.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 80 5.16 5 C 23820 2.51 5 N 6720 2.21 5 O 8200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38820 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "B" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "D" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "E" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "F" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "G" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "H" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "I" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "J" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "K" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "L" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "M" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "N" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "O" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "P" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "Q" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "R" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "S" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "T" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1941 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Time building chain proxies: 8.58, per 1000 atoms: 0.22 Number of scatterers: 38820 At special positions: 0 Unit cell: (137.46, 137.46, 247.95, 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 80 16.00 O 8200 8.00 N 6720 7.00 C 23820 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: 3.51 Conformation dependent library (CDL) restraints added in 1.6 seconds 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10040 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 20 sheets defined 73.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 removed outlier: 3.825A pdb=" N MET A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 272' Processing helix chain 'B' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 101 removed outlier: 3.858A pdb=" N THR B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 272' Processing helix chain 'C' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 59 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 234 removed outlier: 3.868A pdb=" N THR C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU C 240 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 272' Processing helix chain 'D' and resid 9 through 36 removed outlier: 3.827A pdb=" N MET D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE D 110 " --> pdb=" O ASN D 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 267 through 272' Processing helix chain 'E' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR E 58 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE E 110 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 267 through 272' Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA F 59 " --> pdb=" O GLN F 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 removed outlier: 3.697A pdb=" N PHE F 110 " --> pdb=" O ASN F 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE F 272 " --> pdb=" O ILE F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 267 through 272' Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 101 removed outlier: 3.856A pdb=" N THR G 58 " --> pdb=" O ASN G 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP G 67 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE G 110 " --> pdb=" O ASN G 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN G 111 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 3.725A pdb=" N GLU G 240 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN G 263 " --> pdb=" O SER G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE G 272 " --> pdb=" O ILE G 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 267 through 272' Processing helix chain 'H' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 101 removed outlier: 3.856A pdb=" N THR H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE H 110 " --> pdb=" O ASN H 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU H 240 " --> pdb=" O ASP H 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN H 263 " --> pdb=" O SER H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE H 272 " --> pdb=" O ILE H 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 267 through 272' Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.827A pdb=" N MET I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 101 removed outlier: 3.856A pdb=" N THR I 58 " --> pdb=" O ASN I 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA I 59 " --> pdb=" O GLN I 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP I 67 " --> pdb=" O ASN I 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE I 110 " --> pdb=" O ASN I 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN I 263 " --> pdb=" O SER I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE I 272 " --> pdb=" O ILE I 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 267 through 272' Processing helix chain 'J' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET J 13 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR J 58 " --> pdb=" O ASN J 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA J 59 " --> pdb=" O GLN J 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE J 110 " --> pdb=" O ASN J 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN J 111 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 234 removed outlier: 3.868A pdb=" N THR J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE J 272 " --> pdb=" O ILE J 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 267 through 272' Processing helix chain 'K' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET K 13 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 removed outlier: 3.697A pdb=" N PHE K 110 " --> pdb=" O ASN K 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA K 112 " --> pdb=" O ALA K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU K 240 " --> pdb=" O ASP K 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU K 271 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE K 272 " --> pdb=" O ILE K 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 267 through 272' Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET L 13 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR L 58 " --> pdb=" O ASN L 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA L 59 " --> pdb=" O GLN L 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE L 110 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN L 111 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA L 112 " --> pdb=" O ALA L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 234 removed outlier: 3.868A pdb=" N THR L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE L 272 " --> pdb=" O ILE L 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 267 through 272' Processing helix chain 'M' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET M 13 " --> pdb=" O ASN M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR M 58 " --> pdb=" O ASN M 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA M 59 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP M 67 " --> pdb=" O ASN M 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE M 110 " --> pdb=" O ASN M 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN M 111 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA M 112 " --> pdb=" O ALA M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR M 185 " --> pdb=" O ALA M 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU M 240 " --> pdb=" O ASP M 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN M 263 " --> pdb=" O SER M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU M 271 " --> pdb=" O SER M 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE M 272 " --> pdb=" O ILE M 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 267 through 272' Processing helix chain 'N' and resid 9 through 36 removed outlier: 3.825A pdb=" N MET N 13 " --> pdb=" O ASN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 101 removed outlier: 3.858A pdb=" N THR N 58 " --> pdb=" O ASN N 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA N 59 " --> pdb=" O GLN N 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP N 67 " --> pdb=" O ASN N 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE N 110 " --> pdb=" O ASN N 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN N 111 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA N 112 " --> pdb=" O ALA N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU N 240 " --> pdb=" O ASP N 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN N 263 " --> pdb=" O SER N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU N 271 " --> pdb=" O SER N 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE N 272 " --> pdb=" O ILE N 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 267 through 272' Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.825A pdb=" N MET O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR O 58 " --> pdb=" O ASN O 54 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA O 59 " --> pdb=" O GLN O 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP O 67 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER O 68 " --> pdb=" O ALA O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 removed outlier: 3.695A pdb=" N PHE O 110 " --> pdb=" O ASN O 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN O 111 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA O 112 " --> pdb=" O ALA O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 234 removed outlier: 3.868A pdb=" N THR O 185 " --> pdb=" O ALA O 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU O 240 " --> pdb=" O ASP O 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN O 263 " --> pdb=" O SER O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU O 271 " --> pdb=" O SER O 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE O 272 " --> pdb=" O ILE O 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 267 through 272' Processing helix chain 'P' and resid 9 through 36 removed outlier: 3.827A pdb=" N MET P 13 " --> pdb=" O ASN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 101 removed outlier: 3.856A pdb=" N THR P 58 " --> pdb=" O ASN P 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA P 59 " --> pdb=" O GLN P 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP P 67 " --> pdb=" O ASN P 63 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE P 110 " --> pdb=" O ASN P 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN P 111 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA P 112 " --> pdb=" O ALA P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR P 185 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 263 removed outlier: 3.725A pdb=" N GLU P 240 " --> pdb=" O ASP P 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN P 263 " --> pdb=" O SER P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE P 272 " --> pdb=" O ILE P 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 267 through 272' Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR Q 58 " --> pdb=" O ASN Q 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA Q 59 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP Q 67 " --> pdb=" O ASN Q 63 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER Q 68 " --> pdb=" O ALA Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE Q 110 " --> pdb=" O ASN Q 106 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN Q 111 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR Q 185 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU Q 240 " --> pdb=" O ASP Q 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN Q 263 " --> pdb=" O SER Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU Q 271 " --> pdb=" O SER Q 267 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE Q 272 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 267 through 272' Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.827A pdb=" N MET R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA R 59 " --> pdb=" O GLN R 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP R 67 " --> pdb=" O ASN R 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE R 110 " --> pdb=" O ASN R 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN R 111 " --> pdb=" O THR R 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA R 112 " --> pdb=" O ALA R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU R 240 " --> pdb=" O ASP R 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU R 271 " --> pdb=" O SER R 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE R 272 " --> pdb=" O ILE R 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 267 through 272' Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP S 67 " --> pdb=" O ASN S 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER S 68 " --> pdb=" O ALA S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 removed outlier: 3.697A pdb=" N PHE S 110 " --> pdb=" O ASN S 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN S 111 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 263 removed outlier: 3.726A pdb=" N GLU S 240 " --> pdb=" O ASP S 236 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN S 263 " --> pdb=" O SER S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 267 through 272 removed outlier: 3.921A pdb=" N LEU S 271 " --> pdb=" O SER S 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE S 272 " --> pdb=" O ILE S 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 267 through 272' Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.826A pdb=" N MET T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 101 removed outlier: 3.857A pdb=" N THR T 58 " --> pdb=" O ASN T 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER T 68 " --> pdb=" O ALA T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 removed outlier: 3.696A pdb=" N PHE T 110 " --> pdb=" O ASN T 106 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN T 111 " --> pdb=" O THR T 107 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA T 112 " --> pdb=" O ALA T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 234 removed outlier: 3.869A pdb=" N THR T 185 " --> pdb=" O ALA T 181 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 263 removed outlier: 3.727A pdb=" N GLU T 240 " --> pdb=" O ASP T 236 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN T 263 " --> pdb=" O SER T 259 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 272 removed outlier: 3.922A pdb=" N LEU T 271 " --> pdb=" O SER T 267 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE T 272 " --> pdb=" O ILE T 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 267 through 272' 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 149 Processing sheet with id=AA4, first strand: chain 'D' and resid 145 through 149 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 149 Processing sheet with id=AA8, first strand: chain 'H' and resid 145 through 149 Processing sheet with id=AA9, first strand: chain 'I' and resid 145 through 149 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 149 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 149 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 149 3260 hydrogen bonds defined for protein. 9780 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: 6.01 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 11973 1.33 - 1.45: 4282 1.45 - 1.57: 22605 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 39020 Sorted by residual: bond pdb=" CB THR C 206 " pdb=" CG2 THR C 206 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.00e+00 bond pdb=" CB THR G 206 " pdb=" CG2 THR G 206 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB THR I 206 " pdb=" CG2 THR I 206 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB THR K 206 " pdb=" CG2 THR K 206 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CB THR M 206 " pdb=" CG2 THR M 206 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 ... (remaining 39015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 51049 1.73 - 3.46: 1337 3.46 - 5.19: 294 5.19 - 6.92: 80 6.92 - 8.65: 60 Bond angle restraints: 52820 Sorted by residual: angle pdb=" CA LYS K 220 " pdb=" CB LYS K 220 " pdb=" CG LYS K 220 " ideal model delta sigma weight residual 114.10 122.75 -8.65 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA LYS T 220 " pdb=" CB LYS T 220 " pdb=" CG LYS T 220 " ideal model delta sigma weight residual 114.10 122.75 -8.65 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA LYS O 220 " pdb=" CB LYS O 220 " pdb=" CG LYS O 220 " ideal model delta sigma weight residual 114.10 122.75 -8.65 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA LYS Q 220 " pdb=" CB LYS Q 220 " pdb=" CG LYS Q 220 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 angle pdb=" CA LYS H 220 " pdb=" CB LYS H 220 " pdb=" CG LYS H 220 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 ... (remaining 52815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 21595 15.93 - 31.86: 1796 31.86 - 47.79: 329 47.79 - 63.73: 0 63.73 - 79.66: 60 Dihedral angle restraints: 23780 sinusoidal: 8340 harmonic: 15440 Sorted by residual: dihedral pdb=" CA LEU L 232 " pdb=" C LEU L 232 " pdb=" N VAL L 233 " pdb=" CA VAL L 233 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA LEU M 232 " pdb=" C LEU M 232 " pdb=" N VAL M 233 " pdb=" CA VAL M 233 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA LEU R 232 " pdb=" C LEU R 232 " pdb=" N VAL R 233 " pdb=" CA VAL R 233 " ideal model delta harmonic sigma weight residual 180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 23777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4987 0.045 - 0.091: 1422 0.091 - 0.136: 322 0.136 - 0.181: 49 0.181 - 0.226: 20 Chirality restraints: 6800 Sorted by residual: chirality pdb=" CB VAL J 233 " pdb=" CA VAL J 233 " pdb=" CG1 VAL J 233 " pdb=" CG2 VAL J 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL K 233 " pdb=" CA VAL K 233 " pdb=" CG1 VAL K 233 " pdb=" CG2 VAL K 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL T 233 " pdb=" CA VAL T 233 " pdb=" CG1 VAL T 233 " pdb=" CG2 VAL T 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 6797 not shown) Planarity restraints: 6760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 236 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C ASP R 236 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP R 236 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU R 237 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP N 236 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ASP N 236 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP N 236 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU N 237 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 236 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ASP P 236 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP P 236 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU P 237 " 0.013 2.00e-02 2.50e+03 ... (remaining 6757 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1335 2.69 - 3.24: 42520 3.24 - 3.79: 61092 3.79 - 4.35: 73802 4.35 - 4.90: 126436 Nonbonded interactions: 305185 Sorted by model distance: nonbonded pdb=" NZ LYS N 220 " pdb=" OE1 GLN T 17 " model vdw 2.137 3.120 nonbonded pdb=" NZ LYS K 220 " pdb=" OE1 GLN M 17 " model vdw 2.159 3.120 nonbonded pdb=" NZ LYS B 220 " pdb=" OE1 GLN H 17 " model vdw 2.166 3.120 nonbonded pdb=" NZ LYS O 220 " pdb=" OE1 GLN Q 17 " model vdw 2.189 3.120 nonbonded pdb=" OD1 ASP F 102 " pdb=" O THR L 147 " model vdw 2.207 3.040 ... (remaining 305180 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: 0.13 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' } 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 32.850 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.008 0.051 39020 Z= 0.342 Angle : 0.808 8.652 52820 Z= 0.447 Chirality : 0.047 0.226 6800 Planarity : 0.004 0.023 6760 Dihedral : 12.657 79.658 13740 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.11), residues: 5380 helix: 1.66 (0.07), residues: 3940 sheet: -1.88 (0.31), residues: 200 loop : -3.12 (0.13), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 71 PHE 0.012 0.002 PHE B 117 TRP 0.001 0.000 TRP G 49 HIS 0.001 0.000 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00793 (39020) covalent geometry : angle 0.80801 (52820) hydrogen bonds : bond 0.10441 ( 3260) hydrogen bonds : angle 4.58377 ( 9780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1105 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 THR cc_start: 0.8545 (m) cc_final: 0.8305 (m) REVERT: D 92 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8442 (mtmt) REVERT: E 32 ARG cc_start: 0.7445 (tpp80) cc_final: 0.7143 (ttm110) REVERT: E 140 ASP cc_start: 0.7835 (p0) cc_final: 0.7214 (t70) REVERT: F 88 ASP cc_start: 0.7494 (t0) cc_final: 0.7248 (t0) REVERT: G 92 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8302 (mtpt) REVERT: G 123 GLN cc_start: 0.8020 (tp40) cc_final: 0.7608 (mt0) REVERT: G 231 ASN cc_start: 0.8132 (t0) cc_final: 0.7676 (m-40) REVERT: G 240 GLU cc_start: 0.6269 (mp0) cc_final: 0.6062 (mp0) REVERT: H 262 ASN cc_start: 0.7152 (m110) cc_final: 0.6663 (t0) REVERT: I 123 GLN cc_start: 0.7876 (tp40) cc_final: 0.7560 (mt0) REVERT: K 226 ASP cc_start: 0.7605 (m-30) cc_final: 0.7375 (m-30) REVERT: L 55 GLN cc_start: 0.7633 (tp40) cc_final: 0.6935 (tt0) REVERT: L 88 ASP cc_start: 0.8094 (t0) cc_final: 0.7690 (m-30) REVERT: O 231 ASN cc_start: 0.8059 (t0) cc_final: 0.7791 (m-40) REVERT: P 27 THR cc_start: 0.7976 (m) cc_final: 0.7723 (p) REVERT: P 125 GLU cc_start: 0.7657 (tp30) cc_final: 0.6963 (tp30) REVERT: P 184 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7812 (ttpt) REVERT: P 186 MET cc_start: 0.7627 (tpp) cc_final: 0.7165 (tpp) REVERT: Q 110 PHE cc_start: 0.7901 (t80) cc_final: 0.7645 (t80) REVERT: R 43 LYS cc_start: 0.7330 (mtmt) cc_final: 0.7024 (mmtt) REVERT: R 102 ASP cc_start: 0.7737 (t0) cc_final: 0.7496 (t0) REVERT: S 239 LYS cc_start: 0.7947 (mttp) cc_final: 0.7602 (mtmm) REVERT: T 113 LEU cc_start: 0.8316 (mt) cc_final: 0.8114 (mt) REVERT: T 186 MET cc_start: 0.7621 (tpp) cc_final: 0.7000 (tpp) outliers start: 0 outliers final: 0 residues processed: 1105 average time/residue: 0.2190 time to fit residues: 403.8453 Evaluate side-chains 626 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 0.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN B 55 GLN D 248 GLN E 34 ASN E 45 ASN E 248 GLN E 262 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN H 63 ASN H 123 GLN I 45 ASN I 73 GLN J 34 ASN K 245 GLN L 18 ASN M 262 ASN N 4 ASN N 31 GLN ** N 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 GLN P 130 ASN Q 195 GLN Q 251 GLN R 34 ASN R 134 ASN S 123 GLN S 245 GLN T 195 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132269 restraints weight = 64512.372| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.91 r_work: 0.3543 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39020 Z= 0.162 Angle : 0.488 7.302 52820 Z= 0.281 Chirality : 0.035 0.248 6800 Planarity : 0.003 0.047 6760 Dihedral : 3.683 18.179 5460 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.60 % Allowed : 10.98 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.12), residues: 5380 helix: 2.93 (0.08), residues: 3960 sheet: -2.00 (0.26), residues: 240 loop : -2.69 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 32 PHE 0.014 0.001 PHE E 217 TRP 0.009 0.001 TRP Q 49 HIS 0.002 0.000 HIS S 214 Details of bonding type rmsd covalent geometry : bond 0.00301 (39020) covalent geometry : angle 0.48786 (52820) hydrogen bonds : bond 0.07411 ( 3260) hydrogen bonds : angle 3.73450 ( 9780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 738 time to evaluate : 1.382 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: A 122 ASP cc_start: 0.8438 (m-30) cc_final: 0.8191 (m-30) REVERT: A 231 ASN cc_start: 0.8475 (t0) cc_final: 0.8249 (m-40) REVERT: B 43 LYS cc_start: 0.5940 (mmtt) cc_final: 0.5300 (mmtt) REVERT: B 176 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.7904 (p) REVERT: C 95 GLU cc_start: 0.7521 (tt0) cc_final: 0.7229 (tt0) REVERT: C 132 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7964 (mttm) REVERT: D 92 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8276 (mtmt) REVERT: D 122 ASP cc_start: 0.8295 (m-30) cc_final: 0.7800 (m-30) REVERT: E 32 ARG cc_start: 0.7145 (tpp80) cc_final: 0.6832 (ttm110) REVERT: E 88 ASP cc_start: 0.8742 (t0) cc_final: 0.8451 (m-30) REVERT: E 123 GLN cc_start: 0.7382 (tp40) cc_final: 0.7099 (mt0) REVERT: F 231 ASN cc_start: 0.8103 (t0) cc_final: 0.7603 (m-40) REVERT: F 262 ASN cc_start: 0.7675 (m-40) cc_final: 0.7424 (m-40) REVERT: H 14 ILE cc_start: 0.7909 (mt) cc_final: 0.7708 (mm) REVERT: H 262 ASN cc_start: 0.7098 (m110) cc_final: 0.6662 (t0) REVERT: I 123 GLN cc_start: 0.8037 (tp40) cc_final: 0.7639 (mt0) REVERT: J 262 ASN cc_start: 0.8380 (m-40) cc_final: 0.8171 (m-40) REVERT: L 88 ASP cc_start: 0.8883 (t0) cc_final: 0.8073 (m-30) REVERT: M 6 ILE cc_start: 0.8734 (tp) cc_final: 0.8482 (pt) REVERT: M 96 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8280 (mmtp) REVERT: N 250 LYS cc_start: 0.7791 (tttm) cc_final: 0.7482 (ttpt) REVERT: O 43 LYS cc_start: 0.7461 (mtmt) cc_final: 0.7103 (tptt) REVERT: O 80 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8496 (mp) REVERT: O 231 ASN cc_start: 0.8264 (t0) cc_final: 0.7974 (m-40) REVERT: O 262 ASN cc_start: 0.7626 (m110) cc_final: 0.7214 (m-40) REVERT: P 27 THR cc_start: 0.7912 (m) cc_final: 0.7529 (p) REVERT: P 186 MET cc_start: 0.7517 (tpp) cc_final: 0.7119 (tpp) REVERT: P 220 LYS cc_start: 0.7386 (mmtt) cc_final: 0.7111 (mtmt) REVERT: Q 186 MET cc_start: 0.8212 (tpp) cc_final: 0.7948 (tpt) REVERT: R 43 LYS cc_start: 0.8031 (mtmt) cc_final: 0.7576 (mmtt) REVERT: R 102 ASP cc_start: 0.8220 (t0) cc_final: 0.8014 (t0) REVERT: S 239 LYS cc_start: 0.8055 (mttp) cc_final: 0.7650 (mtmm) REVERT: T 96 LYS cc_start: 0.7662 (tppt) cc_final: 0.7398 (tppt) outliers start: 67 outliers final: 38 residues processed: 781 average time/residue: 0.1996 time to fit residues: 267.9817 Evaluate side-chains 648 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 608 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 204 optimal weight: 5.9990 chunk 470 optimal weight: 1.9990 chunk 206 optimal weight: 0.4980 chunk 146 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 365 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 248 GLN E 45 ASN E 248 GLN F 34 ASN G 31 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 73 GLN I 31 GLN J 123 GLN K 31 GLN K 123 GLN L 18 ASN L 34 ASN M 31 GLN ** N 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 262 ASN O 73 GLN O 151 ASN P 73 GLN Q 123 GLN Q 251 GLN R 151 ASN R 248 GLN ** T 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.135381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120825 restraints weight = 64639.238| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.87 r_work: 0.3389 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39020 Z= 0.207 Angle : 0.566 8.758 52820 Z= 0.316 Chirality : 0.037 0.263 6800 Planarity : 0.003 0.050 6760 Dihedral : 3.852 19.259 5460 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.62 % Allowed : 14.50 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.12), residues: 5380 helix: 3.11 (0.08), residues: 3840 sheet: -1.85 (0.27), residues: 240 loop : -2.29 (0.15), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 32 PHE 0.015 0.002 PHE N 117 TRP 0.007 0.001 TRP Q 49 HIS 0.003 0.001 HIS E 214 Details of bonding type rmsd covalent geometry : bond 0.00446 (39020) covalent geometry : angle 0.56616 (52820) hydrogen bonds : bond 0.08832 ( 3260) hydrogen bonds : angle 4.08910 ( 9780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 696 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.5987 (mmtt) cc_final: 0.5455 (mmtt) REVERT: B 136 VAL cc_start: 0.8738 (t) cc_final: 0.8510 (m) REVERT: B 176 THR cc_start: 0.8714 (p) cc_final: 0.8459 (p) REVERT: B 236 ASP cc_start: 0.7300 (t70) cc_final: 0.6539 (t70) REVERT: C 95 GLU cc_start: 0.7650 (tt0) cc_final: 0.7308 (tt0) REVERT: C 132 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7998 (mttm) REVERT: D 88 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: E 88 ASP cc_start: 0.8736 (t0) cc_final: 0.8485 (m-30) REVERT: E 123 GLN cc_start: 0.7830 (tp40) cc_final: 0.7564 (mt0) REVERT: E 136 VAL cc_start: 0.8934 (t) cc_final: 0.8569 (m) REVERT: E 264 SER cc_start: 0.8669 (t) cc_final: 0.8353 (p) REVERT: H 262 ASN cc_start: 0.7480 (m110) cc_final: 0.6824 (t0) REVERT: I 123 GLN cc_start: 0.8281 (tp40) cc_final: 0.7732 (mt0) REVERT: J 262 ASN cc_start: 0.8656 (m-40) cc_final: 0.8448 (m-40) REVERT: L 88 ASP cc_start: 0.8954 (t0) cc_final: 0.8222 (m-30) REVERT: L 102 ASP cc_start: 0.8507 (t0) cc_final: 0.8267 (t0) REVERT: N 232 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8246 (tp) REVERT: N 250 LYS cc_start: 0.7879 (tttm) cc_final: 0.7658 (ttpt) REVERT: O 43 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7948 (tptt) REVERT: O 231 ASN cc_start: 0.8572 (t0) cc_final: 0.8340 (m-40) REVERT: O 262 ASN cc_start: 0.7904 (m110) cc_final: 0.7557 (m110) REVERT: P 27 THR cc_start: 0.7963 (m) cc_final: 0.7623 (p) REVERT: P 140 ASP cc_start: 0.8973 (p0) cc_final: 0.8379 (p0) REVERT: P 220 LYS cc_start: 0.7571 (mmtt) cc_final: 0.7130 (mtmt) REVERT: Q 153 ASP cc_start: 0.8726 (m-30) cc_final: 0.8439 (m-30) REVERT: Q 186 MET cc_start: 0.8457 (tpp) cc_final: 0.8236 (tpt) REVERT: R 43 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7836 (mmtt) REVERT: S 239 LYS cc_start: 0.8055 (mttp) cc_final: 0.7828 (mtmm) REVERT: T 262 ASN cc_start: 0.7239 (m-40) cc_final: 0.6710 (t0) outliers start: 110 outliers final: 70 residues processed: 768 average time/residue: 0.1881 time to fit residues: 253.1482 Evaluate side-chains 648 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 576 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 271 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 27 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 532 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 394 optimal weight: 0.0370 chunk 106 optimal weight: 7.9990 chunk 523 optimal weight: 6.9990 chunk 380 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 427 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 315 optimal weight: 9.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN C 151 ASN D 73 GLN E 45 ASN F 262 ASN G 31 GLN G 73 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN J 4 ASN K 31 GLN K 55 GLN N 31 GLN O 151 ASN Q 251 GLN T 18 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126240 restraints weight = 64211.976| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.86 r_work: 0.3479 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39020 Z= 0.152 Angle : 0.463 6.764 52820 Z= 0.267 Chirality : 0.034 0.249 6800 Planarity : 0.002 0.043 6760 Dihedral : 3.639 17.863 5460 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.43 % Allowed : 16.14 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.12), residues: 5380 helix: 3.43 (0.08), residues: 3860 sheet: -0.95 (0.29), residues: 200 loop : -1.98 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 PHE 0.016 0.001 PHE O 110 TRP 0.009 0.001 TRP Q 49 HIS 0.002 0.000 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00284 (39020) covalent geometry : angle 0.46276 (52820) hydrogen bonds : bond 0.07271 ( 3260) hydrogen bonds : angle 3.69447 ( 9780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 675 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.8404 (t0) cc_final: 0.8167 (m-40) REVERT: B 34 ASN cc_start: 0.7151 (m-40) cc_final: 0.6831 (m-40) REVERT: B 43 LYS cc_start: 0.5963 (mmtt) cc_final: 0.5443 (mmtt) REVERT: B 176 THR cc_start: 0.8571 (p) cc_final: 0.8328 (p) REVERT: C 95 GLU cc_start: 0.7317 (tt0) cc_final: 0.7042 (tt0) REVERT: C 132 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7861 (mttm) REVERT: D 186 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7554 (mmt) REVERT: E 77 ASP cc_start: 0.7144 (m-30) cc_final: 0.6942 (m-30) REVERT: E 88 ASP cc_start: 0.8629 (t0) cc_final: 0.8396 (m-30) REVERT: E 118 ASP cc_start: 0.7764 (m-30) cc_final: 0.7542 (m-30) REVERT: E 123 GLN cc_start: 0.7757 (tp40) cc_final: 0.7556 (mt0) REVERT: E 136 VAL cc_start: 0.8930 (t) cc_final: 0.8553 (m) REVERT: E 264 SER cc_start: 0.8543 (t) cc_final: 0.8200 (p) REVERT: G 39 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8509 (mm) REVERT: J 262 ASN cc_start: 0.8551 (m-40) cc_final: 0.8350 (m110) REVERT: L 88 ASP cc_start: 0.8847 (t0) cc_final: 0.8022 (m-30) REVERT: N 250 LYS cc_start: 0.7940 (tttm) cc_final: 0.7736 (ttpt) REVERT: O 43 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8112 (tptt) REVERT: O 80 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8783 (mp) REVERT: O 231 ASN cc_start: 0.8408 (t0) cc_final: 0.8195 (m-40) REVERT: O 262 ASN cc_start: 0.7911 (m110) cc_final: 0.7544 (m110) REVERT: P 27 THR cc_start: 0.7881 (m) cc_final: 0.7479 (p) REVERT: P 140 ASP cc_start: 0.8975 (p0) cc_final: 0.8470 (p0) REVERT: P 220 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6899 (mtpt) REVERT: R 43 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7809 (mmtt) REVERT: T 95 GLU cc_start: 0.5837 (mm-30) cc_final: 0.5611 (mm-30) REVERT: T 114 LYS cc_start: 0.6269 (mmmt) cc_final: 0.5865 (tptp) REVERT: T 221 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.7967 (tt) outliers start: 102 outliers final: 72 residues processed: 732 average time/residue: 0.1887 time to fit residues: 242.6762 Evaluate side-chains 667 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 591 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain T residue 6 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 243 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 84 optimal weight: 0.1980 chunk 129 optimal weight: 2.9990 chunk 518 optimal weight: 0.8980 chunk 429 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN B 73 GLN D 34 ASN D 251 GLN E 73 GLN G 31 GLN H 31 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 151 ASN H 262 ASN K 34 ASN K 123 GLN L 151 ASN N 34 ASN O 151 ASN R 34 ASN R 134 ASN R 262 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.143129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129042 restraints weight = 63798.553| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.85 r_work: 0.3498 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 39020 Z= 0.139 Angle : 0.442 6.709 52820 Z= 0.255 Chirality : 0.034 0.289 6800 Planarity : 0.002 0.024 6760 Dihedral : 3.482 16.365 5460 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.43 % Allowed : 17.67 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.12), residues: 5380 helix: 3.55 (0.08), residues: 3880 sheet: -0.72 (0.29), residues: 200 loop : -1.89 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 PHE 0.012 0.001 PHE O 110 TRP 0.008 0.001 TRP Q 49 HIS 0.002 0.000 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00246 (39020) covalent geometry : angle 0.44220 (52820) hydrogen bonds : bond 0.06598 ( 3260) hydrogen bonds : angle 3.56375 ( 9780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 649 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.8206 (t0) cc_final: 0.7976 (t0) REVERT: B 31 GLN cc_start: 0.7965 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 34 ASN cc_start: 0.7186 (m-40) cc_final: 0.6815 (m-40) REVERT: B 43 LYS cc_start: 0.5896 (mmtt) cc_final: 0.5365 (mmtt) REVERT: B 176 THR cc_start: 0.8367 (p) cc_final: 0.8028 (p) REVERT: D 122 ASP cc_start: 0.8482 (m-30) cc_final: 0.8143 (m-30) REVERT: D 186 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7461 (mmt) REVERT: E 32 ARG cc_start: 0.7110 (tpp80) cc_final: 0.6893 (ttm-80) REVERT: E 88 ASP cc_start: 0.8599 (t0) cc_final: 0.8377 (m-30) REVERT: E 136 VAL cc_start: 0.8980 (t) cc_final: 0.8588 (m) REVERT: E 264 SER cc_start: 0.8578 (t) cc_final: 0.8206 (p) REVERT: F 43 LYS cc_start: 0.6027 (tptt) cc_final: 0.5726 (tptt) REVERT: G 39 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8335 (mm) REVERT: H 262 ASN cc_start: 0.7056 (m-40) cc_final: 0.6343 (t0) REVERT: K 63 ASN cc_start: 0.8133 (t0) cc_final: 0.7924 (t0) REVERT: K 151 ASN cc_start: 0.8114 (t0) cc_final: 0.7869 (t0) REVERT: L 88 ASP cc_start: 0.8791 (t0) cc_final: 0.7881 (m-30) REVERT: N 250 LYS cc_start: 0.7978 (tttm) cc_final: 0.7769 (ttpt) REVERT: O 43 LYS cc_start: 0.8400 (mtmt) cc_final: 0.8097 (mttm) REVERT: O 80 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8613 (mp) REVERT: O 231 ASN cc_start: 0.8279 (t0) cc_final: 0.8049 (m-40) REVERT: O 262 ASN cc_start: 0.7883 (m110) cc_final: 0.7556 (m110) REVERT: P 27 THR cc_start: 0.7773 (m) cc_final: 0.7382 (p) REVERT: P 125 GLU cc_start: 0.7842 (tp30) cc_final: 0.7120 (tp30) REVERT: P 152 SER cc_start: 0.8192 (t) cc_final: 0.7941 (p) REVERT: P 220 LYS cc_start: 0.7347 (mmtt) cc_final: 0.6762 (mtpt) REVERT: R 43 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7804 (mmtt) REVERT: R 271 LEU cc_start: 0.7329 (tp) cc_final: 0.6862 (mm) REVERT: S 31 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7538 (tt0) REVERT: T 114 LYS cc_start: 0.6132 (mmmt) cc_final: 0.5796 (tptp) REVERT: T 221 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7959 (tt) REVERT: T 262 ASN cc_start: 0.7125 (m-40) cc_final: 0.6459 (t0) outliers start: 102 outliers final: 62 residues processed: 711 average time/residue: 0.1862 time to fit residues: 233.5795 Evaluate side-chains 652 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 586 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 262 ASN Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain T residue 6 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 338 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 308 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 515 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 462 optimal weight: 1.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN F 73 GLN G 31 GLN H 31 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN J 34 ASN J 262 ASN L 151 ASN O 151 ASN R 34 ASN T 34 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122356 restraints weight = 64407.339| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.86 r_work: 0.3407 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39020 Z= 0.182 Angle : 0.519 7.913 52820 Z= 0.292 Chirality : 0.036 0.270 6800 Planarity : 0.002 0.028 6760 Dihedral : 3.653 16.944 5460 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.05 % Allowed : 18.14 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.12), residues: 5380 helix: 3.39 (0.08), residues: 3860 sheet: -0.70 (0.30), residues: 200 loop : -1.87 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 PHE 0.012 0.002 PHE N 117 TRP 0.007 0.001 TRP Q 49 HIS 0.002 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00381 (39020) covalent geometry : angle 0.51872 (52820) hydrogen bonds : bond 0.07971 ( 3260) hydrogen bonds : angle 3.92084 ( 9780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 593 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.8605 (t0) cc_final: 0.8392 (m-40) REVERT: B 43 LYS cc_start: 0.5946 (mmtt) cc_final: 0.5379 (mmtt) REVERT: B 176 THR cc_start: 0.8675 (p) cc_final: 0.8461 (p) REVERT: C 95 GLU cc_start: 0.7421 (tt0) cc_final: 0.7159 (tt0) REVERT: D 122 ASP cc_start: 0.8627 (m-30) cc_final: 0.8336 (m-30) REVERT: D 186 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7566 (mmt) REVERT: E 88 ASP cc_start: 0.8672 (t0) cc_final: 0.8407 (m-30) REVERT: E 118 ASP cc_start: 0.7807 (m-30) cc_final: 0.7537 (m-30) REVERT: E 136 VAL cc_start: 0.9001 (t) cc_final: 0.8592 (m) REVERT: E 264 SER cc_start: 0.8712 (t) cc_final: 0.8341 (p) REVERT: F 43 LYS cc_start: 0.5912 (tptt) cc_final: 0.5682 (tptt) REVERT: F 245 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: G 39 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8376 (mm) REVERT: H 262 ASN cc_start: 0.7094 (m-40) cc_final: 0.6431 (t0) REVERT: K 63 ASN cc_start: 0.8204 (t0) cc_final: 0.7975 (t0) REVERT: L 88 ASP cc_start: 0.8924 (t0) cc_final: 0.8044 (m-30) REVERT: M 245 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7329 (mt0) REVERT: O 43 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8354 (mttm) REVERT: O 80 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8844 (mp) REVERT: O 231 ASN cc_start: 0.8475 (t0) cc_final: 0.8113 (m-40) REVERT: O 262 ASN cc_start: 0.7944 (m110) cc_final: 0.7702 (m110) REVERT: P 27 THR cc_start: 0.7860 (m) cc_final: 0.7477 (p) REVERT: P 125 GLU cc_start: 0.7950 (tp30) cc_final: 0.7112 (tp30) REVERT: P 129 THR cc_start: 0.8592 (t) cc_final: 0.8203 (t) REVERT: P 220 LYS cc_start: 0.7461 (mmtt) cc_final: 0.6904 (mtpt) REVERT: R 43 LYS cc_start: 0.8242 (mtmt) cc_final: 0.7903 (mmtt) REVERT: R 271 LEU cc_start: 0.7321 (tp) cc_final: 0.6887 (mm) REVERT: T 13 MET cc_start: 0.8412 (mpp) cc_final: 0.7813 (mtt) outliers start: 128 outliers final: 94 residues processed: 676 average time/residue: 0.1886 time to fit residues: 224.8293 Evaluate side-chains 650 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 552 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 245 GLN Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain T residue 6 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 353 optimal weight: 7.9990 chunk 423 optimal weight: 8.9990 chunk 468 optimal weight: 0.9990 chunk 340 optimal weight: 7.9990 chunk 414 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 485 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 GLN H 31 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 ASN L 151 ASN O 151 ASN R 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.145546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131546 restraints weight = 63370.526| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.91 r_work: 0.3453 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39020 Z= 0.151 Angle : 0.475 8.566 52820 Z= 0.270 Chirality : 0.035 0.338 6800 Planarity : 0.002 0.021 6760 Dihedral : 3.581 16.813 5460 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.86 % Allowed : 18.79 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.12), residues: 5380 helix: 3.39 (0.08), residues: 3940 sheet: -0.55 (0.30), residues: 200 loop : -1.91 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 32 PHE 0.010 0.001 PHE T 117 TRP 0.007 0.001 TRP T 49 HIS 0.002 0.000 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00283 (39020) covalent geometry : angle 0.47463 (52820) hydrogen bonds : bond 0.07164 ( 3260) hydrogen bonds : angle 3.74112 ( 9780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 593 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LYS cc_start: 0.5916 (mmtt) cc_final: 0.5365 (mmtt) REVERT: B 176 THR cc_start: 0.8567 (p) cc_final: 0.8298 (p) REVERT: D 122 ASP cc_start: 0.8572 (m-30) cc_final: 0.8278 (m-30) REVERT: D 186 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7559 (mmt) REVERT: E 16 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8625 (mt) REVERT: E 88 ASP cc_start: 0.8644 (t0) cc_final: 0.8370 (m-30) REVERT: E 136 VAL cc_start: 0.9027 (t) cc_final: 0.8606 (m) REVERT: E 264 SER cc_start: 0.8715 (t) cc_final: 0.8316 (p) REVERT: G 39 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8230 (mm) REVERT: H 262 ASN cc_start: 0.6906 (m-40) cc_final: 0.6318 (t0) REVERT: K 151 ASN cc_start: 0.8124 (t0) cc_final: 0.7847 (t0) REVERT: L 88 ASP cc_start: 0.8873 (t0) cc_final: 0.7954 (m-30) REVERT: M 245 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7250 (mt0) REVERT: O 43 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8375 (mttm) REVERT: O 80 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8720 (mp) REVERT: O 223 ASP cc_start: 0.7727 (m-30) cc_final: 0.7487 (m-30) REVERT: O 231 ASN cc_start: 0.8355 (t0) cc_final: 0.8034 (m-40) REVERT: O 262 ASN cc_start: 0.7939 (m110) cc_final: 0.7677 (m110) REVERT: P 27 THR cc_start: 0.7749 (m) cc_final: 0.7391 (p) REVERT: P 125 GLU cc_start: 0.7887 (tp30) cc_final: 0.7139 (tp30) REVERT: P 220 LYS cc_start: 0.7294 (mmtt) cc_final: 0.6732 (mtpt) REVERT: R 43 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7874 (mmtt) REVERT: R 271 LEU cc_start: 0.7311 (tp) cc_final: 0.6817 (mm) REVERT: S 31 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7454 (tt0) REVERT: S 253 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7772 (tt) REVERT: T 114 LYS cc_start: 0.6108 (mmmt) cc_final: 0.5823 (tptp) outliers start: 120 outliers final: 91 residues processed: 669 average time/residue: 0.1820 time to fit residues: 216.9057 Evaluate side-chains 657 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 561 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 77 ASP Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 253 LEU Chi-restraints excluded: chain T residue 6 ILE Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 490 optimal weight: 2.9990 chunk 399 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 423 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 66 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 468 optimal weight: 2.9990 chunk 509 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN B 31 GLN G 31 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 151 ASN J 262 ASN L 151 ASN N 73 GLN O 151 ASN P 151 ASN R 34 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129383 restraints weight = 63353.195| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.91 r_work: 0.3447 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39020 Z= 0.164 Angle : 0.505 9.409 52820 Z= 0.284 Chirality : 0.036 0.307 6800 Planarity : 0.002 0.032 6760 Dihedral : 3.606 17.688 5460 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.88 % Allowed : 19.17 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.12), residues: 5380 helix: 3.32 (0.08), residues: 3940 sheet: -1.25 (0.28), residues: 240 loop : -1.85 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 32 PHE 0.011 0.001 PHE H 117 TRP 0.007 0.001 TRP D 49 HIS 0.002 0.000 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00328 (39020) covalent geometry : angle 0.50464 (52820) hydrogen bonds : bond 0.07493 ( 3260) hydrogen bonds : angle 3.83815 ( 9780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 571 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.8339 (m-40) cc_final: 0.7920 (m-40) REVERT: B 43 LYS cc_start: 0.5963 (mmtt) cc_final: 0.5417 (mmtt) REVERT: B 176 THR cc_start: 0.8610 (p) cc_final: 0.8356 (p) REVERT: D 122 ASP cc_start: 0.8593 (m-30) cc_final: 0.8302 (m-30) REVERT: D 186 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7703 (mmt) REVERT: E 16 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8618 (mt) REVERT: E 77 ASP cc_start: 0.7044 (m-30) cc_final: 0.6784 (m-30) REVERT: E 88 ASP cc_start: 0.8661 (t0) cc_final: 0.8398 (m-30) REVERT: E 118 ASP cc_start: 0.7687 (m-30) cc_final: 0.7226 (m-30) REVERT: E 136 VAL cc_start: 0.9042 (t) cc_final: 0.8619 (m) REVERT: E 264 SER cc_start: 0.8690 (t) cc_final: 0.8252 (p) REVERT: G 39 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8261 (mm) REVERT: H 262 ASN cc_start: 0.7000 (m-40) cc_final: 0.6399 (t0) REVERT: L 88 ASP cc_start: 0.8852 (t0) cc_final: 0.7934 (m-30) REVERT: M 245 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7280 (mt0) REVERT: O 43 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8369 (mttm) REVERT: O 80 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8751 (mp) REVERT: O 231 ASN cc_start: 0.8440 (t0) cc_final: 0.8079 (m-40) REVERT: O 262 ASN cc_start: 0.7945 (m110) cc_final: 0.7690 (m110) REVERT: P 27 THR cc_start: 0.7663 (m) cc_final: 0.7329 (p) REVERT: P 125 GLU cc_start: 0.7921 (tp30) cc_final: 0.7064 (tp30) REVERT: P 129 THR cc_start: 0.8444 (t) cc_final: 0.8046 (t) REVERT: P 220 LYS cc_start: 0.7338 (mmtt) cc_final: 0.6759 (mtpt) REVERT: R 43 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7894 (mmtt) REVERT: R 271 LEU cc_start: 0.7335 (tp) cc_final: 0.6859 (mm) REVERT: S 253 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7798 (tt) outliers start: 121 outliers final: 100 residues processed: 647 average time/residue: 0.1863 time to fit residues: 213.8393 Evaluate side-chains 652 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 547 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain S residue 6 ILE Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 253 LEU Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 114 LYS Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 9 optimal weight: 2.9990 chunk 504 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 381 optimal weight: 0.7980 chunk 496 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 434 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 GLN ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN K 34 ASN L 151 ASN R 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129260 restraints weight = 64009.851| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.80 r_work: 0.3450 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39020 Z= 0.156 Angle : 0.496 9.628 52820 Z= 0.279 Chirality : 0.035 0.350 6800 Planarity : 0.002 0.023 6760 Dihedral : 3.595 18.365 5460 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.69 % Allowed : 19.38 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.20 (0.12), residues: 5380 helix: 3.36 (0.08), residues: 3940 sheet: -1.18 (0.28), residues: 240 loop : -1.74 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 32 PHE 0.010 0.001 PHE R 157 TRP 0.008 0.001 TRP D 49 HIS 0.002 0.000 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00302 (39020) covalent geometry : angle 0.49600 (52820) hydrogen bonds : bond 0.07243 ( 3260) hydrogen bonds : angle 3.78475 ( 9780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 575 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.8297 (m-40) cc_final: 0.7874 (m-40) REVERT: B 34 ASN cc_start: 0.7454 (m-40) cc_final: 0.7147 (m-40) REVERT: B 43 LYS cc_start: 0.5909 (mmtt) cc_final: 0.5358 (mmtt) REVERT: B 176 THR cc_start: 0.8519 (p) cc_final: 0.8235 (p) REVERT: C 43 LYS cc_start: 0.6372 (tptt) cc_final: 0.6102 (tptt) REVERT: D 122 ASP cc_start: 0.8539 (m-30) cc_final: 0.8266 (m-30) REVERT: D 186 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7573 (mmt) REVERT: D 251 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6437 (tm130) REVERT: E 16 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8623 (mt) REVERT: E 77 ASP cc_start: 0.7007 (m-30) cc_final: 0.6785 (m-30) REVERT: E 88 ASP cc_start: 0.8644 (t0) cc_final: 0.8392 (m-30) REVERT: E 118 ASP cc_start: 0.7554 (m-30) cc_final: 0.7173 (m-30) REVERT: E 136 VAL cc_start: 0.9026 (t) cc_final: 0.8617 (m) REVERT: E 264 SER cc_start: 0.8605 (t) cc_final: 0.8178 (p) REVERT: G 39 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8272 (mm) REVERT: H 247 LEU cc_start: 0.7858 (mm) cc_final: 0.7466 (mm) REVERT: H 262 ASN cc_start: 0.6994 (m-40) cc_final: 0.6449 (t0) REVERT: L 88 ASP cc_start: 0.8840 (t0) cc_final: 0.7957 (m-30) REVERT: M 245 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7262 (mt0) REVERT: O 43 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8358 (mttm) REVERT: O 80 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8739 (mp) REVERT: O 223 ASP cc_start: 0.7633 (m-30) cc_final: 0.7403 (m-30) REVERT: O 231 ASN cc_start: 0.8382 (t0) cc_final: 0.8060 (m-40) REVERT: O 262 ASN cc_start: 0.7955 (m110) cc_final: 0.7747 (m-40) REVERT: P 27 THR cc_start: 0.7701 (m) cc_final: 0.7396 (p) REVERT: P 125 GLU cc_start: 0.7890 (tp30) cc_final: 0.7080 (tp30) REVERT: P 129 THR cc_start: 0.8477 (t) cc_final: 0.8061 (t) REVERT: P 220 LYS cc_start: 0.7378 (mmtt) cc_final: 0.6834 (mtpt) REVERT: R 43 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7905 (mmtt) REVERT: R 271 LEU cc_start: 0.7345 (tp) cc_final: 0.6897 (mm) REVERT: S 31 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7398 (tt0) REVERT: S 253 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7722 (tt) outliers start: 113 outliers final: 99 residues processed: 648 average time/residue: 0.1870 time to fit residues: 214.2833 Evaluate side-chains 665 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 560 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 253 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 440 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 441 optimal weight: 5.9990 chunk 402 optimal weight: 2.9990 chunk 355 optimal weight: 5.9990 chunk 507 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 468 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN F 151 ASN H 45 ASN H 63 ASN L 151 ASN R 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130078 restraints weight = 63636.152| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.78 r_work: 0.3471 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39020 Z= 0.151 Angle : 0.488 9.868 52820 Z= 0.276 Chirality : 0.035 0.389 6800 Planarity : 0.002 0.037 6760 Dihedral : 3.560 18.873 5460 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.60 % Allowed : 19.40 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.12), residues: 5380 helix: 3.40 (0.08), residues: 3940 sheet: -1.13 (0.28), residues: 240 loop : -1.68 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 32 PHE 0.010 0.001 PHE H 117 TRP 0.009 0.001 TRP D 49 HIS 0.002 0.000 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00287 (39020) covalent geometry : angle 0.48785 (52820) hydrogen bonds : bond 0.07009 ( 3260) hydrogen bonds : angle 3.73256 ( 9780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10760 Ramachandran restraints generated. 5380 Oldfield, 0 Emsley, 5380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 582 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.8274 (m-40) cc_final: 0.7835 (m-40) REVERT: B 31 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7532 (tm-30) REVERT: B 34 ASN cc_start: 0.7358 (m-40) cc_final: 0.7036 (m-40) REVERT: B 43 LYS cc_start: 0.5874 (mmtt) cc_final: 0.5326 (mmtt) REVERT: B 171 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8256 (tt) REVERT: B 176 THR cc_start: 0.8496 (p) cc_final: 0.8194 (p) REVERT: C 43 LYS cc_start: 0.6374 (tptt) cc_final: 0.6094 (tptt) REVERT: D 122 ASP cc_start: 0.8535 (m-30) cc_final: 0.8250 (m-30) REVERT: D 186 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (mmt) REVERT: D 247 LEU cc_start: 0.7072 (mm) cc_final: 0.6520 (mm) REVERT: D 251 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6422 (tm130) REVERT: E 16 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8614 (mt) REVERT: E 77 ASP cc_start: 0.6997 (m-30) cc_final: 0.6759 (m-30) REVERT: E 88 ASP cc_start: 0.8619 (t0) cc_final: 0.8383 (m-30) REVERT: E 118 ASP cc_start: 0.7504 (m-30) cc_final: 0.7129 (m-30) REVERT: E 136 VAL cc_start: 0.9032 (t) cc_final: 0.8623 (m) REVERT: E 264 SER cc_start: 0.8611 (t) cc_final: 0.8186 (p) REVERT: G 39 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8252 (mm) REVERT: H 247 LEU cc_start: 0.7870 (mm) cc_final: 0.7477 (mm) REVERT: H 262 ASN cc_start: 0.6929 (m-40) cc_final: 0.6405 (t0) REVERT: L 88 ASP cc_start: 0.8836 (t0) cc_final: 0.7953 (m-30) REVERT: M 245 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7292 (mt0) REVERT: N 236 ASP cc_start: 0.7839 (p0) cc_final: 0.7558 (p0) REVERT: O 43 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8354 (mttm) REVERT: O 80 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8716 (mp) REVERT: O 223 ASP cc_start: 0.7565 (m-30) cc_final: 0.7291 (m-30) REVERT: O 231 ASN cc_start: 0.8341 (t0) cc_final: 0.8020 (m-40) REVERT: O 262 ASN cc_start: 0.7951 (m110) cc_final: 0.7744 (m-40) REVERT: P 27 THR cc_start: 0.7722 (m) cc_final: 0.7416 (p) REVERT: P 125 GLU cc_start: 0.7919 (tp30) cc_final: 0.7123 (tp30) REVERT: P 129 THR cc_start: 0.8490 (t) cc_final: 0.8074 (t) REVERT: P 220 LYS cc_start: 0.7296 (mmtt) cc_final: 0.6759 (mtpt) REVERT: R 43 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7887 (mmtt) REVERT: R 271 LEU cc_start: 0.7348 (tp) cc_final: 0.6938 (mm) REVERT: S 31 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7427 (tt0) REVERT: S 62 MET cc_start: 0.8754 (mmt) cc_final: 0.8519 (mpp) REVERT: S 253 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7691 (tt) outliers start: 109 outliers final: 99 residues processed: 652 average time/residue: 0.1863 time to fit residues: 214.5754 Evaluate side-chains 660 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 554 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 243 LYS Chi-restraints excluded: chain D residue 251 GLN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 63 ASN Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 45 ASN Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 24 SER Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 269 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 58 THR Chi-restraints excluded: chain N residue 144 THR Chi-restraints excluded: chain N residue 186 MET Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain O residue 80 LEU Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 147 THR Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 267 SER Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain P residue 153 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 43 LYS Chi-restraints excluded: chain Q residue 147 THR Chi-restraints excluded: chain Q residue 163 THR Chi-restraints excluded: chain Q residue 171 LEU Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 163 THR Chi-restraints excluded: chain R residue 171 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 250 LYS Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 163 THR Chi-restraints excluded: chain S residue 234 ASP Chi-restraints excluded: chain S residue 253 LEU Chi-restraints excluded: chain T residue 29 VAL Chi-restraints excluded: chain T residue 84 ASP Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 144 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 232 optimal weight: 1.9990 chunk 404 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 522 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 512 optimal weight: 0.4980 chunk 42 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN E 73 GLN ** G 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN K 34 ASN R 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132171 restraints weight = 63741.786| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.78 r_work: 0.3483 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39020 Z= 0.146 Angle : 0.485 9.898 52820 Z= 0.274 Chirality : 0.035 0.377 6800 Planarity : 0.002 0.021 6760 Dihedral : 3.529 16.209 5460 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.76 % Allowed : 19.52 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.12), residues: 5380 helix: 3.44 (0.08), residues: 3940 sheet: -1.05 (0.29), residues: 240 loop : -1.61 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 32 PHE 0.010 0.001 PHE H 117 TRP 0.008 0.001 TRP D 49 HIS 0.002 0.000 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00271 (39020) covalent geometry : angle 0.48500 (52820) hydrogen bonds : bond 0.06778 ( 3260) hydrogen bonds : angle 3.68418 ( 9780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9425.04 seconds wall clock time: 162 minutes 14.55 seconds (9734.55 seconds total)