Starting phenix.real_space_refine (version: dev) on Tue May 17 08:36:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/05_2022/6xky_22229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/05_2022/6xky_22229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/05_2022/6xky_22229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/05_2022/6xky_22229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/05_2022/6xky_22229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xky_22229/05_2022/6xky_22229.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 38760 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "B" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "C" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "D" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "E" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "F" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "G" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "H" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "I" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "J" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "K" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "L" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "M" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "N" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "O" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "P" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "Q" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "R" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "S" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Chain: "T" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Time building chain proxies: 20.83, per 1000 atoms: 0.54 Number of scatterers: 38760 At special positions: 0 Unit cell: (136.59, 138.33, 248.82, 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 100 16.00 O 8180 8.00 N 6700 7.00 C 23780 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 - 3.50 Amino acid : False - 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: 16.84 Conformation dependent library (CDL) restraints added in 7.0 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 73.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE A 268 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 269 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 270 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP B 67 " --> pdb=" O ASN B 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 removed outlier: 3.649A pdb=" N ASN B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 234 removed outlier: 3.745A pdb=" N THR B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU B 269 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 270 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 59 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 67 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 234 removed outlier: 3.743A pdb=" N THR C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 270 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 36 removed outlier: 3.957A pdb=" N MET D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 101 removed outlier: 3.746A pdb=" N THR D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D 67 " --> pdb=" O ASN D 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 272 removed outlier: 3.685A pdb=" N ILE D 268 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU D 269 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER D 270 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET E 13 " --> pdb=" O ASN E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 101 removed outlier: 3.746A pdb=" N THR E 58 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP E 67 " --> pdb=" O ASN E 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 130 " --> pdb=" O LYS E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE E 268 " --> pdb=" O SER E 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU E 269 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 270 " --> pdb=" O SER E 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA F 59 " --> pdb=" O GLN F 55 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP F 67 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER F 130 " --> pdb=" O LYS F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY F 188 " --> pdb=" O LYS F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE F 268 " --> pdb=" O SER F 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU F 269 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER F 270 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.957A pdb=" N MET G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR G 58 " --> pdb=" O ASN G 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 59 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP G 67 " --> pdb=" O ASN G 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN G 111 " --> pdb=" O THR G 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 234 removed outlier: 3.743A pdb=" N THR G 185 " --> pdb=" O ALA G 181 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN G 263 " --> pdb=" O SER G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE G 268 " --> pdb=" O SER G 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU G 269 " --> pdb=" O SER G 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER G 270 " --> pdb=" O SER G 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET H 13 " --> pdb=" O ASN H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP H 67 " --> pdb=" O ASN H 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN H 111 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 234 removed outlier: 3.745A pdb=" N THR H 185 " --> pdb=" O ALA H 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN H 263 " --> pdb=" O SER H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 272 removed outlier: 3.684A pdb=" N ILE H 268 " --> pdb=" O SER H 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU H 269 " --> pdb=" O SER H 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 270 " --> pdb=" O SER H 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET I 13 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR I 58 " --> pdb=" O ASN I 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA I 59 " --> pdb=" O GLN I 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP I 67 " --> pdb=" O ASN I 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN I 111 " --> pdb=" O THR I 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER I 130 " --> pdb=" O LYS I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR I 185 " --> pdb=" O ALA I 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN I 263 " --> pdb=" O SER I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 272 removed outlier: 3.685A pdb=" N ILE I 268 " --> pdb=" O SER I 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU I 269 " --> pdb=" O SER I 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER I 270 " --> pdb=" O SER I 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET J 13 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 101 removed outlier: 3.744A pdb=" N THR J 58 " --> pdb=" O ASN J 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA J 59 " --> pdb=" O GLN J 55 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP J 67 " --> pdb=" O ASN J 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN J 111 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER J 130 " --> pdb=" O LYS J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY J 188 " --> pdb=" O LYS J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN J 263 " --> pdb=" O SER J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE J 268 " --> pdb=" O SER J 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU J 269 " --> pdb=" O SER J 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER J 270 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 36 removed outlier: 3.957A pdb=" N MET K 13 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP K 67 " --> pdb=" O ASN K 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER K 130 " --> pdb=" O LYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 234 removed outlier: 3.745A pdb=" N THR K 185 " --> pdb=" O ALA K 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY K 188 " --> pdb=" O LYS K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 263 removed outlier: 3.742A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE K 268 " --> pdb=" O SER K 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU K 269 " --> pdb=" O SER K 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER K 270 " --> pdb=" O SER K 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET L 13 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 101 removed outlier: 3.746A pdb=" N THR L 58 " --> pdb=" O ASN L 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA L 59 " --> pdb=" O GLN L 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP L 67 " --> pdb=" O ASN L 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER L 68 " --> pdb=" O ALA L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN L 111 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER L 130 " --> pdb=" O LYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR L 185 " --> pdb=" O ALA L 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 263 removed outlier: 3.742A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 272 removed outlier: 3.684A pdb=" N ILE L 268 " --> pdb=" O SER L 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU L 269 " --> pdb=" O SER L 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER L 270 " --> pdb=" O SER L 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET M 13 " --> pdb=" O ASN M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR M 58 " --> pdb=" O ASN M 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA M 59 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP M 67 " --> pdb=" O ASN M 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN M 111 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER M 130 " --> pdb=" O LYS M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR M 185 " --> pdb=" O ALA M 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY M 188 " --> pdb=" O LYS M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN M 263 " --> pdb=" O SER M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE M 268 " --> pdb=" O SER M 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU M 269 " --> pdb=" O SER M 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER M 270 " --> pdb=" O SER M 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET N 13 " --> pdb=" O ASN N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR N 58 " --> pdb=" O ASN N 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA N 59 " --> pdb=" O GLN N 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP N 67 " --> pdb=" O ASN N 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER N 68 " --> pdb=" O ALA N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 130 removed outlier: 3.649A pdb=" N ASN N 111 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER N 130 " --> pdb=" O LYS N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN N 263 " --> pdb=" O SER N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE N 268 " --> pdb=" O SER N 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU N 269 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER N 270 " --> pdb=" O SER N 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET O 13 " --> pdb=" O ASN O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR O 58 " --> pdb=" O ASN O 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA O 59 " --> pdb=" O GLN O 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP O 67 " --> pdb=" O ASN O 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER O 68 " --> pdb=" O ALA O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 removed outlier: 3.652A pdb=" N ASN O 111 " --> pdb=" O THR O 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER O 130 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 234 removed outlier: 3.743A pdb=" N THR O 185 " --> pdb=" O ALA O 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY O 188 " --> pdb=" O LYS O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN O 263 " --> pdb=" O SER O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 272 removed outlier: 3.682A pdb=" N ILE O 268 " --> pdb=" O SER O 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU O 269 " --> pdb=" O SER O 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER O 270 " --> pdb=" O SER O 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET P 13 " --> pdb=" O ASN P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR P 58 " --> pdb=" O ASN P 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA P 59 " --> pdb=" O GLN P 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP P 67 " --> pdb=" O ASN P 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 removed outlier: 3.649A pdb=" N ASN P 111 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER P 130 " --> pdb=" O LYS P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 234 removed outlier: 3.745A pdb=" N THR P 185 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY P 188 " --> pdb=" O LYS P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN P 263 " --> pdb=" O SER P 259 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 272 removed outlier: 3.684A pdb=" N ILE P 268 " --> pdb=" O SER P 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU P 269 " --> pdb=" O SER P 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER P 270 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET Q 13 " --> pdb=" O ASN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 101 removed outlier: 3.744A pdb=" N THR Q 58 " --> pdb=" O ASN Q 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA Q 59 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP Q 67 " --> pdb=" O ASN Q 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER Q 68 " --> pdb=" O ALA Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 removed outlier: 3.651A pdb=" N ASN Q 111 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER Q 130 " --> pdb=" O LYS Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR Q 185 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY Q 188 " --> pdb=" O LYS Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN Q 263 " --> pdb=" O SER Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE Q 268 " --> pdb=" O SER Q 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU Q 269 " --> pdb=" O SER Q 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER Q 270 " --> pdb=" O SER Q 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 36 removed outlier: 3.959A pdb=" N MET R 13 " --> pdb=" O ASN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR R 58 " --> pdb=" O ASN R 54 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA R 59 " --> pdb=" O GLN R 55 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP R 67 " --> pdb=" O ASN R 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN R 111 " --> pdb=" O THR R 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER R 130 " --> pdb=" O LYS R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY R 188 " --> pdb=" O LYS R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN R 263 " --> pdb=" O SER R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE R 268 " --> pdb=" O SER R 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU R 269 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER R 270 " --> pdb=" O SER R 267 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 101 removed outlier: 3.744A pdb=" N THR S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP S 67 " --> pdb=" O ASN S 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER S 68 " --> pdb=" O ALA S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN S 111 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER S 130 " --> pdb=" O LYS S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY S 188 " --> pdb=" O LYS S 184 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 263 removed outlier: 3.741A pdb=" N ALA S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN S 263 " --> pdb=" O SER S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 272 removed outlier: 3.683A pdb=" N ILE S 268 " --> pdb=" O SER S 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU S 269 " --> pdb=" O SER S 266 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER S 270 " --> pdb=" O SER S 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 36 removed outlier: 3.958A pdb=" N MET T 13 " --> pdb=" O ASN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 101 removed outlier: 3.745A pdb=" N THR T 58 " --> pdb=" O ASN T 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER T 68 " --> pdb=" O ALA T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 removed outlier: 3.650A pdb=" N ASN T 111 " --> pdb=" O THR T 107 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER T 130 " --> pdb=" O LYS T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 181 through 234 removed outlier: 3.744A pdb=" N THR T 185 " --> pdb=" O ALA T 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY T 188 " --> pdb=" O LYS T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 263 removed outlier: 3.740A pdb=" N ALA T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN T 263 " --> pdb=" O SER T 259 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 272 removed outlier: 3.684A pdb=" N ILE T 268 " --> pdb=" O SER T 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU T 269 " --> pdb=" O SER T 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER T 270 " --> pdb=" O SER T 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 149 Processing sheet with id=AA2, first strand: chain 'B' and resid 145 through 149 Processing sheet with id=AA3, first strand: chain 'C' and resid 145 through 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 3340 hydrogen bonds defined for protein. 9900 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: 14.01 Time building geometry restraints manager: 17.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9398 1.33 - 1.45: 6425 1.45 - 1.57: 22957 1.57 - 1.69: 0 1.69 - 1.80: 180 Bond restraints: 38960 Sorted by residual: bond pdb=" CA SER H 101 " pdb=" C SER H 101 " ideal model delta sigma weight residual 1.523 1.495 0.027 1.41e-02 5.03e+03 3.78e+00 bond pdb=" CA SER B 101 " pdb=" C SER B 101 " ideal model delta sigma weight residual 1.523 1.495 0.027 1.41e-02 5.03e+03 3.73e+00 bond pdb=" CA SER N 101 " pdb=" C SER N 101 " ideal model delta sigma weight residual 1.523 1.495 0.027 1.41e-02 5.03e+03 3.71e+00 bond pdb=" CA SER P 101 " pdb=" C SER P 101 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.41e-02 5.03e+03 3.69e+00 bond pdb=" CA SER Q 101 " pdb=" C SER Q 101 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.41e-02 5.03e+03 3.66e+00 ... (remaining 38955 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.49: 124 106.49 - 113.39: 23997 113.39 - 120.29: 13830 120.29 - 127.19: 14709 127.19 - 134.09: 60 Bond angle restraints: 52720 Sorted by residual: angle pdb=" C LEU R 232 " pdb=" N VAL R 233 " pdb=" CA VAL R 233 " ideal model delta sigma weight residual 122.69 118.21 4.48 1.49e+00 4.50e-01 9.04e+00 angle pdb=" C THR K 172 " pdb=" N THR K 173 " pdb=" CA THR K 173 " ideal model delta sigma weight residual 121.31 125.78 -4.47 1.49e+00 4.50e-01 9.02e+00 angle pdb=" C LEU J 232 " pdb=" N VAL J 233 " pdb=" CA VAL J 233 " ideal model delta sigma weight residual 122.69 118.23 4.46 1.49e+00 4.50e-01 8.97e+00 angle pdb=" C THR T 172 " pdb=" N THR T 173 " pdb=" CA THR T 173 " ideal model delta sigma weight residual 121.31 125.77 -4.46 1.49e+00 4.50e-01 8.97e+00 angle pdb=" C LEU O 232 " pdb=" N VAL O 233 " pdb=" CA VAL O 233 " ideal model delta sigma weight residual 122.69 118.23 4.46 1.49e+00 4.50e-01 8.94e+00 ... (remaining 52715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.75: 21902 12.75 - 25.50: 1404 25.50 - 38.25: 294 38.25 - 51.00: 100 51.00 - 63.75: 60 Dihedral angle restraints: 23760 sinusoidal: 8320 harmonic: 15440 Sorted by residual: dihedral pdb=" CA LEU H 232 " pdb=" C LEU H 232 " pdb=" N VAL H 233 " pdb=" CA VAL H 233 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 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 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU O 232 " pdb=" C LEU O 232 " pdb=" N VAL O 233 " pdb=" CA VAL O 233 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 23757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 4003 0.027 - 0.053: 1918 0.053 - 0.080: 596 0.080 - 0.107: 243 0.107 - 0.133: 20 Chirality restraints: 6780 Sorted by residual: chirality pdb=" CA VAL N 159 " pdb=" N VAL N 159 " pdb=" C VAL N 159 " pdb=" CB VAL N 159 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 159 " pdb=" N VAL A 159 " pdb=" C VAL A 159 " pdb=" CB VAL A 159 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL J 159 " pdb=" N VAL J 159 " pdb=" C VAL J 159 " pdb=" CB VAL J 159 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 6777 not shown) Planarity restraints: 6740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR J 196 " 0.004 2.00e-02 2.50e+03 8.03e-03 6.45e-01 pdb=" C THR J 196 " -0.014 2.00e-02 2.50e+03 pdb=" O THR J 196 " 0.005 2.00e-02 2.50e+03 pdb=" N ALA J 197 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 196 " 0.004 2.00e-02 2.50e+03 7.87e-03 6.19e-01 pdb=" C THR R 196 " -0.014 2.00e-02 2.50e+03 pdb=" O THR R 196 " 0.005 2.00e-02 2.50e+03 pdb=" N ALA R 197 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR S 196 " -0.004 2.00e-02 2.50e+03 7.84e-03 6.14e-01 pdb=" C THR S 196 " 0.014 2.00e-02 2.50e+03 pdb=" O THR S 196 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA S 197 " -0.005 2.00e-02 2.50e+03 ... (remaining 6737 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 9 2.25 - 2.91: 16607 2.91 - 3.58: 57126 3.58 - 4.24: 82288 4.24 - 4.90: 147466 Nonbonded interactions: 303496 Sorted by model distance: nonbonded pdb=" OD2 ASP K 234 " pdb=" OG SER N 5 " model vdw 1.588 2.440 nonbonded pdb=" OD2 ASP P 234 " pdb=" OG SER Q 5 " model vdw 1.647 2.440 nonbonded pdb=" OD2 ASP D 234 " pdb=" OG SER E 5 " model vdw 1.649 2.440 nonbonded pdb=" OD2 ASP L 234 " pdb=" OG SER M 5 " model vdw 1.650 2.440 nonbonded pdb=" OD2 ASP H 234 " pdb=" OG SER J 5 " model vdw 1.669 2.440 ... (remaining 303491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 23780 2.51 5 N 6700 2.21 5 O 8180 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.410 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: 0.030 Extract box with map and model: 10.840 Check model and map are aligned: 0.620 Convert atoms to be neutral: 0.340 Process input model: 99.860 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 0.006 0.030 38960 Z= 0.371 Angle : 0.546 5.184 52720 Z= 0.342 Chirality : 0.035 0.133 6780 Planarity : 0.002 0.008 6740 Dihedral : 10.036 63.748 13720 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.11), residues: 5380 helix: 3.04 (0.08), residues: 3980 sheet: -0.00 (0.35), residues: 200 loop : -2.67 (0.14), residues: 1200 *********************** 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 962 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 942 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 945 average time/residue: 0.4512 time to fit residues: 712.7134 Evaluate side-chains 607 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 594 time to evaluate : 4.499 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3149 time to fit residues: 13.8840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 2.9990 chunk 409 optimal weight: 7.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 423 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 257 optimal weight: 0.6980 chunk 315 optimal weight: 0.6980 chunk 490 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 123 GLN A 195 GLN A 222 GLN A 248 GLN B 195 GLN C 123 GLN C 222 GLN C 231 ASN C 252 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 151 ASN D 222 GLN E 123 GLN E 151 ASN E 222 GLN F 30 GLN F 111 ASN F 151 ASN F 222 GLN G 30 GLN G 151 ASN G 222 GLN H 31 GLN H 55 GLN H 151 ASN H 222 GLN H 248 GLN H 252 GLN I 151 ASN J 222 GLN K 31 GLN K 222 GLN L 30 GLN L 34 ASN L 55 GLN L 123 GLN L 252 GLN M 31 GLN M 222 GLN M 256 GLN M 262 ASN N 151 ASN N 222 GLN O 73 GLN O 106 ASN O 222 GLN O 256 GLN P 31 GLN P 34 ASN P 73 GLN P 222 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 222 GLN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN R 222 GLN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 GLN S 151 ASN S 252 GLN ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 151 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 38960 Z= 0.192 Angle : 0.413 5.235 52720 Z= 0.245 Chirality : 0.032 0.180 6780 Planarity : 0.002 0.025 6740 Dihedral : 3.536 17.877 5460 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.12), residues: 5380 helix: 3.74 (0.08), residues: 3880 sheet: 0.13 (0.35), residues: 200 loop : -1.89 (0.16), residues: 1300 *********************** 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 720 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 652 time to evaluate : 4.468 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 39 residues processed: 693 average time/residue: 0.4214 time to fit residues: 506.6628 Evaluate side-chains 581 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 542 time to evaluate : 4.474 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3292 time to fit residues: 30.7167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 408 optimal weight: 8.9990 chunk 333 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 491 optimal weight: 1.9990 chunk 530 optimal weight: 2.9990 chunk 437 optimal weight: 3.9990 chunk 487 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 134 ASN A 222 GLN B 134 ASN C 151 ASN C 222 GLN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 34 ASN D 106 ASN E 4 ASN E 63 ASN E 123 GLN E 222 GLN F 30 GLN F 222 GLN G 30 GLN G 134 ASN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN I 30 GLN I 151 ASN J 222 GLN K 31 GLN M 31 GLN M 123 GLN M 245 GLN N 34 ASN N 106 ASN N 151 ASN O 73 GLN P 17 GLN P 55 GLN P 73 GLN P 222 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 GLN Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN S 222 GLN T 31 GLN T 55 GLN T 151 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 38960 Z= 0.225 Angle : 0.422 5.576 52720 Z= 0.250 Chirality : 0.032 0.182 6780 Planarity : 0.002 0.021 6740 Dihedral : 3.546 17.699 5460 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.12), residues: 5380 helix: 3.67 (0.08), residues: 3880 sheet: 0.12 (0.35), residues: 200 loop : -1.82 (0.17), residues: 1300 *********************** 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 657 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 574 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 43 residues processed: 639 average time/residue: 0.4142 time to fit residues: 460.3556 Evaluate side-chains 565 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 522 time to evaluate : 4.672 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.3216 time to fit residues: 32.6251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 3.9990 chunk 369 optimal weight: 8.9990 chunk 254 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 chunk 493 optimal weight: 1.9990 chunk 521 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 467 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 252 GLN B 134 ASN C 73 GLN C 123 GLN C 151 ASN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN F 222 GLN G 30 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN I 30 GLN I 123 GLN I 151 ASN K 31 GLN L 30 GLN N 106 ASN N 151 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 GLN P 73 GLN P 248 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 GLN Q 151 ASN Q 252 GLN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN T 31 GLN T 151 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 38960 Z= 0.176 Angle : 0.388 5.876 52720 Z= 0.232 Chirality : 0.031 0.179 6780 Planarity : 0.002 0.017 6740 Dihedral : 3.434 17.022 5460 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.12), residues: 5380 helix: 3.86 (0.08), residues: 3880 sheet: 0.18 (0.34), residues: 200 loop : -1.75 (0.17), residues: 1300 *********************** 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 623 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 566 time to evaluate : 4.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 603 average time/residue: 0.4207 time to fit residues: 446.7327 Evaluate side-chains 546 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 517 time to evaluate : 4.929 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3335 time to fit residues: 24.5505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 0.6980 chunk 296 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 388 optimal weight: 0.0470 chunk 215 optimal weight: 30.0000 chunk 445 optimal weight: 0.9990 chunk 360 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 6.9990 chunk 468 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 overall best weight: 1.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN C 123 GLN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 GLN G 30 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN I 123 GLN I 151 ASN K 7 ASN L 30 GLN L 106 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 GLN ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN T 31 GLN T 151 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 38960 Z= 0.183 Angle : 0.392 5.882 52720 Z= 0.233 Chirality : 0.031 0.175 6780 Planarity : 0.002 0.020 6740 Dihedral : 3.410 17.135 5460 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.12), residues: 5380 helix: 3.83 (0.08), residues: 3900 sheet: 0.18 (0.34), residues: 200 loop : -1.66 (0.17), residues: 1280 *********************** 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 584 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 536 time to evaluate : 4.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 563 average time/residue: 0.4116 time to fit residues: 404.5850 Evaluate side-chains 539 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 511 time to evaluate : 4.438 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3195 time to fit residues: 23.1574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 522 optimal weight: 10.0000 chunk 433 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN C 73 GLN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN F 151 ASN G 30 GLN G 222 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN I 73 GLN I 123 GLN I 151 ASN J 30 GLN K 7 ASN L 30 GLN M 31 GLN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 ASN O 73 GLN ** O 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 252 GLN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN T 31 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 38960 Z= 0.281 Angle : 0.454 5.712 52720 Z= 0.265 Chirality : 0.034 0.177 6780 Planarity : 0.002 0.027 6740 Dihedral : 3.653 18.212 5460 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.12), residues: 5380 helix: 3.52 (0.08), residues: 3900 sheet: 0.06 (0.34), residues: 200 loop : -1.74 (0.17), residues: 1280 *********************** 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 562 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 515 time to evaluate : 4.573 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 27 residues processed: 549 average time/residue: 0.4183 time to fit residues: 403.0432 Evaluate side-chains 519 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 492 time to evaluate : 4.537 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3207 time to fit residues: 22.7829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 297 optimal weight: 100.0000 chunk 381 optimal weight: 1.9990 chunk 295 optimal weight: 5.9990 chunk 439 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 chunk 520 optimal weight: 3.9990 chunk 325 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN G 30 GLN G 222 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 GLN I 151 ASN K 7 ASN L 30 GLN M 31 GLN N 106 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN P 123 GLN ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 252 GLN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 ASN R 222 GLN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 GLN S 151 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 38960 Z= 0.259 Angle : 0.440 6.824 52720 Z= 0.259 Chirality : 0.033 0.176 6780 Planarity : 0.002 0.023 6740 Dihedral : 3.636 18.170 5460 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.12), residues: 5380 helix: 3.52 (0.08), residues: 3900 sheet: 0.06 (0.34), residues: 200 loop : -1.75 (0.17), residues: 1280 *********************** 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 542 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 513 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 528 average time/residue: 0.4159 time to fit residues: 385.3847 Evaluate side-chains 514 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 497 time to evaluate : 4.638 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3338 time to fit residues: 17.3488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 310 optimal weight: 0.0470 chunk 156 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 330 optimal weight: 0.9990 chunk 354 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 409 optimal weight: 4.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN B 73 GLN B 134 ASN C 106 ASN C 123 GLN C 231 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN F 151 ASN G 30 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN K 7 ASN M 245 GLN N 106 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 GLN P 31 GLN P 73 GLN P 123 GLN ** P 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN Q 252 GLN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 222 GLN ** S 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN ** S 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 38960 Z= 0.137 Angle : 0.370 6.598 52720 Z= 0.222 Chirality : 0.030 0.171 6780 Planarity : 0.002 0.014 6740 Dihedral : 3.304 16.061 5460 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.12), residues: 5380 helix: 4.05 (0.08), residues: 3900 sheet: 0.27 (0.33), residues: 200 loop : -1.55 (0.18), residues: 1280 *********************** 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 616 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 592 time to evaluate : 4.886 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 608 average time/residue: 0.4382 time to fit residues: 467.3167 Evaluate side-chains 523 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 513 time to evaluate : 4.456 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3504 time to fit residues: 12.4569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 4.9990 chunk 498 optimal weight: 5.9990 chunk 454 optimal weight: 0.8980 chunk 485 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 438 optimal weight: 0.9990 chunk 458 optimal weight: 9.9990 chunk 483 optimal weight: 1.9990 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 34 ASN A 123 GLN B 195 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN D 151 ASN D 222 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN J 55 GLN K 7 ASN K 151 ASN L 30 GLN M 30 GLN M 151 ASN M 245 GLN N 222 GLN ** P 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 GLN ** P 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN S 222 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 38960 Z= 0.174 Angle : 0.393 6.310 52720 Z= 0.234 Chirality : 0.031 0.202 6780 Planarity : 0.002 0.019 6740 Dihedral : 3.339 17.419 5460 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.07 (0.12), residues: 5380 helix: 4.03 (0.08), residues: 3880 sheet: 0.29 (0.34), residues: 200 loop : -1.49 (0.18), residues: 1300 *********************** 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 538 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 525 time to evaluate : 4.598 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 530 average time/residue: 0.4293 time to fit residues: 401.2694 Evaluate side-chains 513 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 504 time to evaluate : 4.226 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3223 time to fit residues: 11.1166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 8.9990 chunk 512 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 243 optimal weight: 0.6980 chunk 356 optimal weight: 4.9990 chunk 537 optimal weight: 1.9990 chunk 495 optimal weight: 2.9990 chunk 428 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN B 134 ASN C 123 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 GLN I 151 ASN L 30 GLN M 245 GLN P 31 GLN P 73 GLN P 245 GLN ** P 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN S 222 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 38960 Z= 0.204 Angle : 0.412 6.232 52720 Z= 0.245 Chirality : 0.032 0.170 6780 Planarity : 0.002 0.018 6740 Dihedral : 3.440 17.284 5460 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.12), residues: 5380 helix: 3.84 (0.08), residues: 3900 sheet: 0.27 (0.34), residues: 200 loop : -1.55 (0.18), residues: 1280 ********************** 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 509 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 499 time to evaluate : 4.703 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 504 average time/residue: 0.4354 time to fit residues: 384.9248 Evaluate side-chains 498 residues out of total 4200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 494 time to evaluate : 4.861 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3601 time to fit residues: 9.1636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 0.0270 chunk 456 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 chunk 395 optimal weight: 0.0870 chunk 63 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 429 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 440 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 overall best weight: 2.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 123 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN K 248 GLN L 30 GLN M 245 GLN P 73 GLN P 245 GLN ** P 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 151 ASN R 34 ASN ** R 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.102991 restraints weight = 49368.032| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.19 r_work: 0.3048 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.3022 rms_B_bonded: 1.19 restraints_weight: 0.1250 r_work: 0.3005 rms_B_bonded: 1.39 restraints_weight: 0.0625 r_work: 0.2985 rms_B_bonded: 1.67 restraints_weight: 0.0312 r_work: 0.2959 rms_B_bonded: 2.06 restraints_weight: 0.0156 r_work: 0.2926 rms_B_bonded: 2.59 restraints_weight: 0.0078 r_work: 0.2886 rms_B_bonded: 3.29 restraints_weight: 0.0039 r_work: 0.2836 rms_B_bonded: 4.22 restraints_weight: 0.0020 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 38960 Z= 0.242 Angle : 0.438 6.228 52720 Z= 0.258 Chirality : 0.033 0.171 6780 Planarity : 0.002 0.023 6740 Dihedral : 3.551 17.377 5460 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.12), residues: 5380 helix: 3.69 (0.08), residues: 3900 sheet: 0.22 (0.34), residues: 200 loop : -1.60 (0.18), residues: 1280 =============================================================================== Job complete usr+sys time: 8026.74 seconds wall clock time: 146 minutes 55.49 seconds (8815.49 seconds total)