Starting phenix.real_space_refine on Tue Aug 26 14:39:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xky_22229/08_2025/6xky_22229.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xky_22229/08_2025/6xky_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/cci-nas-00/data/ceres_data/6xky_22229/08_2025/6xky_22229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xky_22229/08_2025/6xky_22229.map" model { file = "/net/cci-nas-00/data/ceres_data/6xky_22229/08_2025/6xky_22229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xky_22229/08_2025/6xky_22229.cif" } 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 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= 0.005 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 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. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38760 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1938 Classifications: {'peptide': 271} Link IDs: {'TRANS': 270} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T Time building chain proxies: 3.54, per 1000 atoms: 0.09 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 - 3.00 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: 3.06 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.65 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: 5.62 Time building geometry restraints manager: 4.05 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: 0.00 - 1.04: 49615 1.04 - 2.07: 2627 2.07 - 3.11: 318 3.11 - 4.15: 81 4.15 - 5.18: 79 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 3.040 nonbonded pdb=" OD2 ASP P 234 " pdb=" OG SER Q 5 " model vdw 1.647 3.040 nonbonded pdb=" OD2 ASP D 234 " pdb=" OG SER E 5 " model vdw 1.649 3.040 nonbonded pdb=" OD2 ASP L 234 " pdb=" OG SER M 5 " model vdw 1.650 3.040 nonbonded pdb=" OD2 ASP H 234 " pdb=" OG SER J 5 " model vdw 1.669 3.040 ... (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 Time spend for trying shortcut: 0.09 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: 2.110 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 24.410 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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= 0.258 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 : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.48 % Allowed : 4.29 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 71 PHE 0.007 0.001 PHE G 117 TRP 0.003 0.001 TRP F 49 HIS 0.001 0.000 HIS O 214 Details of bonding type rmsd covalent geometry : bond 0.00568 (38960) covalent geometry : angle 0.54602 (52720) hydrogen bonds : bond 0.14050 ( 3340) hydrogen bonds : angle 4.30468 ( 9900) *********************** 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 to be fit. rotamer outliers: 20 poor density : 942 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8086 (m-40) cc_final: 0.7857 (m-40) REVERT: A 132 LYS cc_start: 0.8416 (mtmm) cc_final: 0.8140 (mttt) REVERT: A 171 LEU cc_start: 0.8016 (mt) cc_final: 0.7770 (tp) REVERT: B 25 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7671 (mt-10) REVERT: B 134 ASN cc_start: 0.8575 (t0) cc_final: 0.8317 (t0) REVERT: B 226 ASP cc_start: 0.7646 (m-30) cc_final: 0.7333 (m-30) REVERT: C 125 GLU cc_start: 0.7886 (tp30) cc_final: 0.7573 (mm-30) REVERT: D 123 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7274 (mt0) REVERT: D 140 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: E 30 GLN cc_start: 0.8201 (mt0) cc_final: 0.7786 (mt0) REVERT: E 34 ASN cc_start: 0.7415 (m-40) cc_final: 0.7129 (m-40) REVERT: E 63 ASN cc_start: 0.8213 (t0) cc_final: 0.8000 (t0) REVERT: E 123 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7736 (mt0) REVERT: F 213 THR cc_start: 0.8912 (m) cc_final: 0.8695 (p) REVERT: G 27 THR cc_start: 0.8814 (m) cc_final: 0.8478 (p) REVERT: G 31 GLN cc_start: 0.7749 (tp40) cc_final: 0.7539 (tt0) REVERT: H 236 ASP cc_start: 0.8223 (t0) cc_final: 0.8016 (t0) REVERT: I 119 SER cc_start: 0.8387 (t) cc_final: 0.8000 (m) REVERT: I 174 THR cc_start: 0.7594 (p) cc_final: 0.7361 (p) REVERT: J 41 SER cc_start: 0.8725 (t) cc_final: 0.8470 (m) REVERT: J 239 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7602 (mmtt) REVERT: M 31 GLN cc_start: 0.8034 (tp40) cc_final: 0.7762 (tm-30) REVERT: M 32 ARG cc_start: 0.8481 (mtt90) cc_final: 0.8185 (mtt180) REVERT: M 119 SER cc_start: 0.8770 (t) cc_final: 0.8409 (p) REVERT: N 27 THR cc_start: 0.8673 (m) cc_final: 0.8399 (p) REVERT: N 151 ASN cc_start: 0.7918 (t0) cc_final: 0.7592 (t0) REVERT: O 116 ASP cc_start: 0.7431 (m-30) cc_final: 0.7112 (m-30) REVERT: R 151 ASN cc_start: 0.8055 (t0) cc_final: 0.7539 (t0) REVERT: S 77 ASP cc_start: 0.7229 (m-30) cc_final: 0.6935 (m-30) REVERT: S 132 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7779 (ptpp) REVERT: S 179 THR cc_start: 0.9089 (p) cc_final: 0.8864 (t) REVERT: S 223 ASP cc_start: 0.7640 (m-30) cc_final: 0.7343 (m-30) outliers start: 20 outliers final: 13 residues processed: 945 average time/residue: 0.1880 time to fit residues: 300.1194 Evaluate side-chains 621 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 607 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 140 ASP Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain M residue 140 ASP Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain P residue 140 ASP Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain S residue 140 ASP Chi-restraints excluded: chain T residue 140 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 0.0970 chunk 223 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 D 55 GLN D 151 ASN D 222 GLN E 151 ASN E 222 GLN F 30 GLN F 151 ASN F 222 GLN G 30 GLN G 222 GLN H 31 GLN H 55 GLN 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 222 GLN M 256 GLN M 262 ASN N 222 GLN O 106 ASN O 222 GLN O 256 GLN P 31 GLN P 34 ASN P 222 GLN Q 151 ASN Q 222 GLN R 222 GLN S 123 GLN S 151 ASN S 252 GLN T 151 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109625 restraints weight = 49426.189| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.20 r_work: 0.3086 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 38960 Z= 0.156 Angle : 0.415 5.321 52720 Z= 0.248 Chirality : 0.032 0.174 6780 Planarity : 0.002 0.024 6740 Dihedral : 3.553 17.472 5488 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.17 % Allowed : 8.60 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.64 (0.12), residues: 5380 helix: 3.75 (0.08), residues: 3880 sheet: 0.17 (0.35), residues: 200 loop : -1.81 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 PHE 0.009 0.001 PHE B 117 TRP 0.008 0.001 TRP F 49 HIS 0.002 0.001 HIS P 214 Details of bonding type rmsd covalent geometry : bond 0.00261 (38960) covalent geometry : angle 0.41510 (52720) hydrogen bonds : bond 0.08075 ( 3340) hydrogen bonds : angle 3.44764 ( 9900) *********************** 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 710 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 661 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8008 (mt-10) REVERT: B 103 CYS cc_start: 0.8025 (m) cc_final: 0.7740 (m) REVERT: B 263 GLN cc_start: 0.8141 (pt0) cc_final: 0.7830 (pp30) REVERT: C 123 GLN cc_start: 0.8240 (mt0) cc_final: 0.7955 (mt0) REVERT: D 41 SER cc_start: 0.8922 (t) cc_final: 0.8660 (p) REVERT: D 123 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7717 (mt0) REVERT: D 250 LYS cc_start: 0.8825 (tttm) cc_final: 0.8362 (ttpt) REVERT: E 35 THR cc_start: 0.8756 (t) cc_final: 0.8553 (t) REVERT: G 26 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8808 (tt) REVERT: G 31 GLN cc_start: 0.8276 (tp40) cc_final: 0.7909 (tt0) REVERT: G 134 ASN cc_start: 0.8565 (t0) cc_final: 0.8269 (t160) REVERT: H 31 GLN cc_start: 0.8595 (tp40) cc_final: 0.8197 (tp-100) REVERT: H 123 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7633 (mt0) REVERT: I 119 SER cc_start: 0.8618 (t) cc_final: 0.8296 (m) REVERT: J 26 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8492 (tt) REVERT: J 41 SER cc_start: 0.9028 (t) cc_final: 0.8780 (m) REVERT: J 151 ASN cc_start: 0.8151 (t0) cc_final: 0.7918 (t0) REVERT: M 31 GLN cc_start: 0.8370 (tp40) cc_final: 0.7772 (tm-30) REVERT: M 140 ASP cc_start: 0.7893 (m-30) cc_final: 0.7470 (t0) REVERT: M 151 ASN cc_start: 0.7936 (t0) cc_final: 0.7405 (t0) REVERT: M 153 ASP cc_start: 0.6955 (m-30) cc_final: 0.6600 (m-30) REVERT: N 27 THR cc_start: 0.8628 (m) cc_final: 0.8301 (p) REVERT: O 151 ASN cc_start: 0.7956 (t0) cc_final: 0.7747 (t0) REVERT: P 31 GLN cc_start: 0.7735 (mt0) cc_final: 0.7381 (mm-40) REVERT: P 41 SER cc_start: 0.8877 (m) cc_final: 0.8599 (p) REVERT: P 140 ASP cc_start: 0.7477 (m-30) cc_final: 0.7257 (m-30) REVERT: P 251 GLN cc_start: 0.8220 (tt0) cc_final: 0.8003 (tt0) REVERT: Q 26 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8703 (tt) REVERT: Q 31 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7974 (tp-100) REVERT: R 151 ASN cc_start: 0.8438 (t0) cc_final: 0.8038 (t0) REVERT: S 179 THR cc_start: 0.9113 (p) cc_final: 0.8847 (t) REVERT: T 151 ASN cc_start: 0.7749 (t0) cc_final: 0.7447 (t0) REVERT: T 245 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7958 (mm110) outliers start: 49 outliers final: 24 residues processed: 692 average time/residue: 0.2053 time to fit residues: 247.1803 Evaluate side-chains 588 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 561 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 284 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 189 optimal weight: 40.0000 chunk 159 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 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 30 GLN A 222 GLN B 134 ASN C 18 ASN C 222 GLN C 231 ASN F 30 GLN G 30 GLN G 151 ASN H 151 ASN H 252 GLN I 30 GLN I 151 ASN K 31 GLN N 34 ASN N 106 ASN N 151 ASN O 73 GLN Q 123 GLN Q 151 ASN R 151 ASN R 231 ASN S 151 ASN S 222 GLN T 31 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.107210 restraints weight = 48944.276| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.20 r_work: 0.3051 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2384 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= 0.156 Angle : 0.405 6.639 52720 Z= 0.242 Chirality : 0.032 0.179 6780 Planarity : 0.002 0.019 6740 Dihedral : 3.443 19.396 5460 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.14 % Allowed : 9.98 % Favored : 87.88 % 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 aren not related in a simple way. whole: 3.73 (0.12), residues: 5380 helix: 3.79 (0.08), residues: 3880 sheet: 0.21 (0.35), residues: 200 loop : -1.67 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 32 PHE 0.010 0.001 PHE J 117 TRP 0.007 0.001 TRP T 49 HIS 0.003 0.001 HIS P 214 Details of bonding type rmsd covalent geometry : bond 0.00276 (38960) covalent geometry : angle 0.40524 (52720) hydrogen bonds : bond 0.08138 ( 3340) hydrogen bonds : angle 3.40841 ( 9900) *********************** 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 684 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 594 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7731 (t0) cc_final: 0.7488 (m-30) REVERT: B 103 CYS cc_start: 0.8003 (m) cc_final: 0.7778 (m) REVERT: C 123 GLN cc_start: 0.8342 (mt0) cc_final: 0.7989 (mt0) REVERT: D 41 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8668 (p) REVERT: D 123 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7942 (mt0) REVERT: D 250 LYS cc_start: 0.8764 (tttm) cc_final: 0.8286 (ttpt) REVERT: E 35 THR cc_start: 0.8914 (t) cc_final: 0.8694 (t) REVERT: E 95 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7824 (tt0) REVERT: E 134 ASN cc_start: 0.8855 (t0) cc_final: 0.8341 (t0) REVERT: F 26 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8781 (tt) REVERT: G 26 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8850 (tt) REVERT: G 31 GLN cc_start: 0.8250 (tp40) cc_final: 0.7890 (tt0) REVERT: G 134 ASN cc_start: 0.8599 (t0) cc_final: 0.8289 (t160) REVERT: H 26 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8547 (tt) REVERT: H 31 GLN cc_start: 0.8554 (tp40) cc_final: 0.7910 (tt0) REVERT: H 123 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7862 (mt0) REVERT: I 119 SER cc_start: 0.8621 (t) cc_final: 0.8306 (m) REVERT: J 26 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8542 (tt) REVERT: J 41 SER cc_start: 0.8994 (t) cc_final: 0.8780 (m) REVERT: M 31 GLN cc_start: 0.8290 (tp40) cc_final: 0.7871 (tm-30) REVERT: M 123 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7883 (mm-40) REVERT: M 140 ASP cc_start: 0.7819 (m-30) cc_final: 0.7462 (t0) REVERT: M 151 ASN cc_start: 0.7973 (t0) cc_final: 0.7476 (t0) REVERT: M 153 ASP cc_start: 0.7011 (m-30) cc_final: 0.6718 (m-30) REVERT: M 263 GLN cc_start: 0.7742 (pt0) cc_final: 0.7298 (mm-40) REVERT: N 27 THR cc_start: 0.8550 (m) cc_final: 0.8169 (p) REVERT: O 92 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7852 (mtmm) REVERT: O 151 ASN cc_start: 0.8043 (t0) cc_final: 0.7594 (t0) REVERT: P 31 GLN cc_start: 0.7874 (mt0) cc_final: 0.7440 (mm-40) REVERT: P 251 GLN cc_start: 0.8344 (tt0) cc_final: 0.8111 (tt0) REVERT: Q 26 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8723 (tt) REVERT: Q 123 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: R 31 GLN cc_start: 0.8104 (tp40) cc_final: 0.7780 (tp40) REVERT: R 151 ASN cc_start: 0.8462 (t0) cc_final: 0.8087 (t0) REVERT: S 179 THR cc_start: 0.9167 (p) cc_final: 0.8935 (t) outliers start: 90 outliers final: 51 residues processed: 661 average time/residue: 0.1835 time to fit residues: 212.6579 Evaluate side-chains 602 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 544 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 123 GLN Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 70 optimal weight: 5.9990 chunk 399 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 chunk 489 optimal weight: 4.9990 chunk 426 optimal weight: 0.7980 chunk 529 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 494 optimal weight: 7.9990 chunk 478 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 34 ASN A 123 GLN A 252 GLN C 231 ASN E 4 ASN F 30 GLN F 222 GLN G 30 GLN H 252 GLN I 30 GLN I 151 ASN J 222 GLN K 31 GLN L 30 GLN N 106 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 ASN P 222 GLN Q 123 GLN Q 151 ASN R 34 ASN S 151 ASN T 31 GLN T 151 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.120664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.103868 restraints weight = 49514.642| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.19 r_work: 0.3004 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38960 Z= 0.173 Angle : 0.427 5.914 52720 Z= 0.253 Chirality : 0.033 0.177 6780 Planarity : 0.002 0.019 6740 Dihedral : 3.546 17.848 5460 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.21 % Allowed : 10.62 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.12), residues: 5380 helix: 3.64 (0.08), residues: 3900 sheet: 0.14 (0.34), residues: 200 loop : -1.60 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 71 PHE 0.011 0.001 PHE P 177 TRP 0.005 0.001 TRP I 49 HIS 0.004 0.001 HIS P 214 Details of bonding type rmsd covalent geometry : bond 0.00337 (38960) covalent geometry : angle 0.42745 (52720) hydrogen bonds : bond 0.08818 ( 3340) hydrogen bonds : angle 3.54602 ( 9900) *********************** 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 671 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 578 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7816 (t0) cc_final: 0.7526 (m-30) REVERT: A 171 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7381 (mp) REVERT: B 226 ASP cc_start: 0.8164 (m-30) cc_final: 0.7757 (m-30) REVERT: B 263 GLN cc_start: 0.8168 (pt0) cc_final: 0.7784 (pp30) REVERT: C 123 GLN cc_start: 0.8352 (mt0) cc_final: 0.8030 (mt0) REVERT: D 41 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8701 (p) REVERT: D 123 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8020 (mt0) REVERT: G 26 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8833 (tt) REVERT: G 31 GLN cc_start: 0.8287 (tp40) cc_final: 0.7919 (tt0) REVERT: G 134 ASN cc_start: 0.8619 (t0) cc_final: 0.8373 (t0) REVERT: H 31 GLN cc_start: 0.8544 (tp40) cc_final: 0.8061 (tt0) REVERT: H 38 LYS cc_start: 0.8379 (mttp) cc_final: 0.7965 (mtpt) REVERT: H 123 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7900 (mt0) REVERT: I 119 SER cc_start: 0.8622 (t) cc_final: 0.8231 (m) REVERT: J 26 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8524 (tt) REVERT: J 41 SER cc_start: 0.8987 (t) cc_final: 0.8774 (m) REVERT: K 239 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7911 (mttp) REVERT: M 31 GLN cc_start: 0.8317 (tp40) cc_final: 0.7890 (tm-30) REVERT: M 123 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7683 (mt0) REVERT: M 140 ASP cc_start: 0.7875 (m-30) cc_final: 0.7502 (t0) REVERT: M 151 ASN cc_start: 0.7999 (t0) cc_final: 0.7655 (t0) REVERT: M 245 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7700 (mm110) REVERT: M 263 GLN cc_start: 0.7795 (pt0) cc_final: 0.7314 (mm-40) REVERT: N 24 SER cc_start: 0.8856 (m) cc_final: 0.8559 (t) REVERT: N 27 THR cc_start: 0.8579 (m) cc_final: 0.8141 (p) REVERT: O 151 ASN cc_start: 0.8072 (t0) cc_final: 0.7596 (t0) REVERT: P 31 GLN cc_start: 0.7952 (mt0) cc_final: 0.7499 (mm-40) REVERT: P 251 GLN cc_start: 0.8413 (tt0) cc_final: 0.8207 (tt0) REVERT: Q 26 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8768 (tt) REVERT: R 151 ASN cc_start: 0.8524 (t0) cc_final: 0.8154 (t0) REVERT: S 179 THR cc_start: 0.9166 (p) cc_final: 0.8949 (t) REVERT: T 151 ASN cc_start: 0.7604 (t0) cc_final: 0.7062 (t0) REVERT: T 153 ASP cc_start: 0.8155 (p0) cc_final: 0.7882 (p0) outliers start: 93 outliers final: 64 residues processed: 643 average time/residue: 0.1729 time to fit residues: 195.5479 Evaluate side-chains 606 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 537 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 255 VAL Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 129 THR Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 368 optimal weight: 5.9990 chunk 391 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 chunk 389 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 417 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 484 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN C 231 ASN E 63 ASN E 222 GLN F 151 ASN G 30 GLN H 252 GLN I 30 GLN I 73 GLN I 123 GLN I 151 ASN K 7 ASN L 30 GLN N 106 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN P 248 GLN Q 123 GLN Q 151 ASN R 34 ASN S 151 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.102741 restraints weight = 49685.639| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.18 r_work: 0.2988 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38960 Z= 0.179 Angle : 0.430 5.479 52720 Z= 0.255 Chirality : 0.033 0.177 6780 Planarity : 0.002 0.020 6740 Dihedral : 3.569 17.990 5460 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.40 % Allowed : 10.98 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.12), residues: 5380 helix: 3.59 (0.08), residues: 3900 sheet: 0.12 (0.34), residues: 200 loop : -1.58 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 71 PHE 0.011 0.001 PHE P 177 TRP 0.005 0.001 TRP I 49 HIS 0.003 0.001 HIS P 214 Details of bonding type rmsd covalent geometry : bond 0.00355 (38960) covalent geometry : angle 0.42973 (52720) hydrogen bonds : bond 0.08988 ( 3340) hydrogen bonds : angle 3.58830 ( 9900) *********************** 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 645 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 544 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLN cc_start: 0.8106 (mt0) cc_final: 0.7864 (tp-100) REVERT: A 171 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7463 (mp) REVERT: B 125 GLU cc_start: 0.8286 (tp30) cc_final: 0.7913 (tp30) REVERT: B 226 ASP cc_start: 0.8206 (m-30) cc_final: 0.7821 (m-30) REVERT: D 41 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8699 (p) REVERT: D 107 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7530 (p) REVERT: D 123 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8073 (mt0) REVERT: F 26 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8772 (tt) REVERT: G 26 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8830 (tt) REVERT: G 31 GLN cc_start: 0.8289 (tp40) cc_final: 0.7911 (tt0) REVERT: G 134 ASN cc_start: 0.8625 (t0) cc_final: 0.8382 (t0) REVERT: H 31 GLN cc_start: 0.8556 (tp40) cc_final: 0.8074 (tt0) REVERT: H 38 LYS cc_start: 0.8463 (mttp) cc_final: 0.7984 (mtpt) REVERT: I 119 SER cc_start: 0.8625 (t) cc_final: 0.8226 (m) REVERT: J 26 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8525 (tt) REVERT: J 41 SER cc_start: 0.8970 (t) cc_final: 0.8750 (m) REVERT: K 239 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7952 (mttp) REVERT: L 66 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8471 (mtmt) REVERT: M 31 GLN cc_start: 0.8332 (tp40) cc_final: 0.7910 (tm-30) REVERT: M 123 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7692 (mt0) REVERT: M 134 ASN cc_start: 0.8987 (t0) cc_final: 0.8571 (t0) REVERT: M 140 ASP cc_start: 0.7856 (m-30) cc_final: 0.7590 (t0) REVERT: M 245 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7685 (mm110) REVERT: M 263 GLN cc_start: 0.7856 (pt0) cc_final: 0.7326 (mm-40) REVERT: N 24 SER cc_start: 0.8867 (m) cc_final: 0.8605 (t) REVERT: N 27 THR cc_start: 0.8554 (m) cc_final: 0.8118 (p) REVERT: O 151 ASN cc_start: 0.7992 (t0) cc_final: 0.7742 (t0) REVERT: O 252 GLN cc_start: 0.8114 (mt0) cc_final: 0.7820 (mt0) REVERT: P 251 GLN cc_start: 0.8396 (tt0) cc_final: 0.8188 (tt0) REVERT: Q 26 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8761 (tt) REVERT: R 151 ASN cc_start: 0.8578 (t0) cc_final: 0.8252 (t0) REVERT: S 14 ILE cc_start: 0.8583 (mm) cc_final: 0.8319 (mp) REVERT: S 179 THR cc_start: 0.9166 (p) cc_final: 0.8956 (t) outliers start: 101 outliers final: 74 residues processed: 617 average time/residue: 0.1838 time to fit residues: 197.8824 Evaluate side-chains 616 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 535 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 255 VAL Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 129 THR Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 213 optimal weight: 3.9990 chunk 472 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 380 optimal weight: 10.0000 chunk 369 optimal weight: 0.7980 chunk 321 optimal weight: 1.9990 chunk 501 optimal weight: 9.9990 chunk 459 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 151 ASN E 231 ASN F 151 ASN G 30 GLN H 252 GLN I 151 ASN K 7 ASN L 30 GLN M 151 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN Q 151 ASN R 34 ASN S 151 ASN T 106 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104448 restraints weight = 49531.173| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.18 r_work: 0.3011 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38960 Z= 0.167 Angle : 0.413 6.016 52720 Z= 0.247 Chirality : 0.032 0.176 6780 Planarity : 0.002 0.018 6740 Dihedral : 3.520 17.463 5460 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.67 % Allowed : 11.05 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.65 (0.12), residues: 5380 helix: 3.67 (0.08), residues: 3900 sheet: 0.13 (0.34), residues: 200 loop : -1.55 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 71 PHE 0.010 0.001 PHE P 177 TRP 0.005 0.001 TRP I 49 HIS 0.003 0.001 HIS P 214 Details of bonding type rmsd covalent geometry : bond 0.00320 (38960) covalent geometry : angle 0.41288 (52720) hydrogen bonds : bond 0.08597 ( 3340) hydrogen bonds : angle 3.50574 ( 9900) *********************** 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 672 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 560 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7381 (mp) REVERT: B 125 GLU cc_start: 0.8290 (tp30) cc_final: 0.7853 (tp30) REVERT: B 226 ASP cc_start: 0.8112 (m-30) cc_final: 0.7714 (m-30) REVERT: D 41 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8680 (p) REVERT: D 123 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8058 (mt0) REVERT: F 26 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8736 (tt) REVERT: G 26 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8834 (tt) REVERT: G 31 GLN cc_start: 0.8259 (tp40) cc_final: 0.7889 (tt0) REVERT: G 134 ASN cc_start: 0.8618 (t0) cc_final: 0.8384 (t0) REVERT: H 26 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8528 (tt) REVERT: H 31 GLN cc_start: 0.8512 (tp40) cc_final: 0.8026 (tt0) REVERT: H 38 LYS cc_start: 0.8469 (mttp) cc_final: 0.7978 (mtpt) REVERT: I 119 SER cc_start: 0.8620 (t) cc_final: 0.8225 (m) REVERT: J 26 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8525 (tt) REVERT: J 41 SER cc_start: 0.8981 (t) cc_final: 0.8740 (m) REVERT: K 239 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7940 (mttp) REVERT: L 66 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8441 (mtmt) REVERT: M 123 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7928 (mm-40) REVERT: M 134 ASN cc_start: 0.8967 (t0) cc_final: 0.8567 (t0) REVERT: M 140 ASP cc_start: 0.7825 (m-30) cc_final: 0.7596 (t0) REVERT: M 245 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7693 (mm110) REVERT: M 263 GLN cc_start: 0.7834 (pt0) cc_final: 0.7358 (mm-40) REVERT: N 24 SER cc_start: 0.8847 (m) cc_final: 0.8618 (t) REVERT: N 27 THR cc_start: 0.8493 (m) cc_final: 0.8063 (p) REVERT: O 252 GLN cc_start: 0.8107 (mt0) cc_final: 0.7797 (mt0) REVERT: Q 5 SER cc_start: 0.7455 (OUTLIER) cc_final: 0.7137 (p) REVERT: Q 26 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8763 (tt) REVERT: R 151 ASN cc_start: 0.8529 (t0) cc_final: 0.8184 (t0) REVERT: S 14 ILE cc_start: 0.8506 (mm) cc_final: 0.8235 (mp) REVERT: S 179 THR cc_start: 0.9167 (p) cc_final: 0.8950 (t) REVERT: T 106 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7111 (m110) REVERT: T 151 ASN cc_start: 0.7650 (t0) cc_final: 0.7213 (m-40) outliers start: 112 outliers final: 82 residues processed: 639 average time/residue: 0.1894 time to fit residues: 212.3224 Evaluate side-chains 615 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 524 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain J residue 267 SER Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain Q residue 103 CYS Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 41 SER Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 255 VAL Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain T residue 103 CYS Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 129 THR Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 223 optimal weight: 8.9990 chunk 186 optimal weight: 0.9980 chunk 122 optimal weight: 0.0870 chunk 235 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 462 optimal weight: 0.9990 chunk 527 optimal weight: 0.0870 chunk 524 optimal weight: 7.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN C 123 GLN C 231 ASN D 151 ASN G 30 GLN H 252 GLN I 123 GLN I 151 ASN M 30 GLN M 151 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 151 ASN P 31 GLN Q 151 ASN R 34 ASN S 123 GLN S 151 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.113616 restraints weight = 48431.064| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.17 r_work: 0.3141 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 38960 Z= 0.137 Angle : 0.376 6.807 52720 Z= 0.226 Chirality : 0.031 0.173 6780 Planarity : 0.002 0.019 6740 Dihedral : 3.295 15.707 5460 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.17 % Allowed : 11.83 % Favored : 86.00 % 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 aren not related in a simple way. whole: 4.07 (0.12), residues: 5380 helix: 3.99 (0.08), residues: 3900 sheet: 0.30 (0.34), residues: 200 loop : -1.45 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 32 PHE 0.009 0.001 PHE J 117 TRP 0.007 0.001 TRP I 49 HIS 0.002 0.000 HIS P 214 Details of bonding type rmsd covalent geometry : bond 0.00224 (38960) covalent geometry : angle 0.37586 (52720) hydrogen bonds : bond 0.06948 ( 3340) hydrogen bonds : angle 3.14261 ( 9900) *********************** 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 688 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 597 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ASN cc_start: 0.8958 (t0) cc_final: 0.8672 (t0) REVERT: A 171 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7316 (mp) REVERT: C 30 GLN cc_start: 0.8154 (mt0) cc_final: 0.7880 (mt0) REVERT: D 41 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8619 (p) REVERT: D 123 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7913 (mt0) REVERT: F 26 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8783 (tt) REVERT: G 26 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8855 (tt) REVERT: G 31 GLN cc_start: 0.8175 (tp40) cc_final: 0.7723 (tt0) REVERT: G 92 LYS cc_start: 0.8119 (mttt) cc_final: 0.7865 (mmmt) REVERT: G 134 ASN cc_start: 0.8551 (t0) cc_final: 0.8272 (t160) REVERT: H 31 GLN cc_start: 0.8363 (tp40) cc_final: 0.7890 (tt0) REVERT: H 38 LYS cc_start: 0.8471 (mttp) cc_final: 0.7972 (mtpt) REVERT: H 84 ASP cc_start: 0.7535 (t0) cc_final: 0.7131 (m-30) REVERT: H 123 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7208 (tp-100) REVERT: I 119 SER cc_start: 0.8576 (t) cc_final: 0.8112 (m) REVERT: J 26 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8547 (tt) REVERT: J 41 SER cc_start: 0.8964 (t) cc_final: 0.8700 (m) REVERT: J 93 MET cc_start: 0.8864 (mtp) cc_final: 0.8659 (mtm) REVERT: K 239 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7868 (mttp) REVERT: M 123 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7853 (mm-40) REVERT: M 140 ASP cc_start: 0.7802 (m-30) cc_final: 0.7557 (t0) REVERT: M 263 GLN cc_start: 0.7665 (pt0) cc_final: 0.7233 (mm-40) REVERT: N 24 SER cc_start: 0.8775 (m) cc_final: 0.8575 (t) REVERT: N 27 THR cc_start: 0.8396 (m) cc_final: 0.7870 (p) REVERT: O 26 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8699 (tt) REVERT: O 119 SER cc_start: 0.8639 (t) cc_final: 0.8396 (p) REVERT: Q 5 SER cc_start: 0.7628 (OUTLIER) cc_final: 0.7348 (p) REVERT: Q 26 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8715 (tt) REVERT: Q 31 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7769 (tp-100) REVERT: Q 179 THR cc_start: 0.9221 (p) cc_final: 0.8910 (t) REVERT: R 26 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8908 (tt) REVERT: R 151 ASN cc_start: 0.8523 (t0) cc_final: 0.8153 (t0) REVERT: S 179 THR cc_start: 0.9123 (p) cc_final: 0.8899 (t) REVERT: T 151 ASN cc_start: 0.7618 (t0) cc_final: 0.7121 (m-40) outliers start: 91 outliers final: 52 residues processed: 664 average time/residue: 0.1890 time to fit residues: 220.4674 Evaluate side-chains 598 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 537 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 138 ILE Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 138 ILE Chi-restraints excluded: chain T residue 176 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 507 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 288 optimal weight: 2.9990 chunk 357 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 468 optimal weight: 2.9990 chunk 347 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN C 123 GLN D 18 ASN D 151 ASN E 73 GLN G 30 GLN G 222 GLN H 252 GLN I 151 ASN K 248 GLN L 30 GLN M 30 GLN M 151 ASN M 245 GLN N 151 ASN N 222 GLN O 151 ASN P 55 GLN P 245 GLN Q 123 GLN Q 151 ASN R 34 ASN S 151 ASN T 106 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.120382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103481 restraints weight = 49024.401| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.19 r_work: 0.3001 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2827 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= 0.179 Angle : 0.436 7.560 52720 Z= 0.257 Chirality : 0.033 0.206 6780 Planarity : 0.002 0.022 6740 Dihedral : 3.502 18.432 5460 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.17 % Allowed : 12.57 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.12), residues: 5380 helix: 3.72 (0.08), residues: 3900 sheet: 0.22 (0.34), residues: 200 loop : -1.48 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 71 PHE 0.011 0.001 PHE D 177 TRP 0.004 0.001 TRP I 49 HIS 0.003 0.001 HIS P 214 Details of bonding type rmsd covalent geometry : bond 0.00365 (38960) covalent geometry : angle 0.43638 (52720) hydrogen bonds : bond 0.08782 ( 3340) hydrogen bonds : angle 3.54190 ( 9900) *********************** 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 635 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 544 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7880 (t0) cc_final: 0.7541 (m-30) REVERT: A 134 ASN cc_start: 0.8759 (t0) cc_final: 0.8366 (t0) REVERT: A 171 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7343 (mp) REVERT: B 125 GLU cc_start: 0.8283 (tp30) cc_final: 0.7884 (tp30) REVERT: B 226 ASP cc_start: 0.8115 (m-30) cc_final: 0.7699 (m-30) REVERT: C 26 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8614 (tt) REVERT: C 234 ASP cc_start: 0.8109 (m-30) cc_final: 0.7775 (t0) REVERT: D 123 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8077 (mt0) REVERT: F 26 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8703 (tt) REVERT: F 62 MET cc_start: 0.8580 (mtm) cc_final: 0.8229 (mtp) REVERT: G 26 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8844 (tt) REVERT: G 31 GLN cc_start: 0.8246 (tp40) cc_final: 0.7846 (tt0) REVERT: H 31 GLN cc_start: 0.8494 (tp40) cc_final: 0.8002 (tt0) REVERT: H 38 LYS cc_start: 0.8501 (mttp) cc_final: 0.7999 (mtpt) REVERT: I 119 SER cc_start: 0.8580 (t) cc_final: 0.8168 (m) REVERT: J 26 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8513 (tt) REVERT: J 41 SER cc_start: 0.8975 (t) cc_final: 0.8720 (m) REVERT: K 239 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7958 (mttp) REVERT: M 123 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7930 (mm-40) REVERT: M 239 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7911 (ttpt) REVERT: M 263 GLN cc_start: 0.7801 (pt0) cc_final: 0.7312 (mm-40) REVERT: N 24 SER cc_start: 0.8848 (m) cc_final: 0.8593 (t) REVERT: N 27 THR cc_start: 0.8448 (m) cc_final: 0.7977 (p) REVERT: O 252 GLN cc_start: 0.8103 (mt0) cc_final: 0.7806 (mt0) REVERT: P 251 GLN cc_start: 0.8387 (tt0) cc_final: 0.8186 (tt0) REVERT: Q 5 SER cc_start: 0.7740 (OUTLIER) cc_final: 0.7506 (p) REVERT: Q 26 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8727 (tt) REVERT: Q 179 THR cc_start: 0.9232 (p) cc_final: 0.8897 (t) REVERT: R 151 ASN cc_start: 0.8499 (t0) cc_final: 0.8174 (t0) REVERT: S 179 THR cc_start: 0.9144 (p) cc_final: 0.8925 (t) REVERT: T 106 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.6673 (m110) REVERT: T 151 ASN cc_start: 0.7557 (t0) cc_final: 0.7310 (m-40) outliers start: 91 outliers final: 66 residues processed: 613 average time/residue: 0.1775 time to fit residues: 192.1722 Evaluate side-chains 592 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 518 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 106 ASN Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 103 CYS Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 106 ASN Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain J residue 123 GLN Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 106 ASN Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 138 ILE Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 119 SER Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 246 SER Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 124 ILE Chi-restraints excluded: chain N residue 179 THR Chi-restraints excluded: chain N residue 246 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain P residue 119 SER Chi-restraints excluded: chain P residue 138 ILE Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 138 ILE Chi-restraints excluded: chain Q residue 245 GLN Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 140 ASP Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 103 CYS Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 106 ASN Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.212 > 50: distance: 25 - 45: 12.904 distance: 29 - 54: 8.083 distance: 35 - 65: 14.972 distance: 39 - 45: 12.409 distance: 40 - 73: 12.720 distance: 45 - 46: 11.783 distance: 46 - 47: 14.145 distance: 46 - 49: 8.968 distance: 47 - 48: 15.818 distance: 48 - 81: 29.696 distance: 49 - 50: 6.151 distance: 50 - 51: 10.569 distance: 51 - 52: 3.732 distance: 51 - 53: 4.210 distance: 54 - 55: 7.576 distance: 55 - 56: 4.847 distance: 55 - 58: 4.890 distance: 56 - 57: 6.879 distance: 56 - 65: 9.291 distance: 57 - 88: 15.244 distance: 58 - 59: 10.308 distance: 59 - 60: 7.896 distance: 60 - 61: 11.083 distance: 61 - 62: 9.125 distance: 62 - 63: 9.317 distance: 62 - 64: 9.169 distance: 65 - 66: 13.918 distance: 66 - 67: 8.577 distance: 66 - 69: 4.993 distance: 67 - 68: 21.193 distance: 67 - 73: 8.209 distance: 69 - 70: 9.089 distance: 69 - 71: 14.282 distance: 70 - 72: 18.300 distance: 73 - 74: 5.491 distance: 74 - 75: 7.997 distance: 75 - 76: 14.137 distance: 75 - 81: 26.058 distance: 77 - 78: 5.931 distance: 78 - 79: 5.417 distance: 78 - 80: 9.574 distance: 81 - 82: 21.067 distance: 82 - 83: 7.284 distance: 82 - 85: 15.276 distance: 83 - 84: 35.729 distance: 83 - 88: 27.584 distance: 85 - 86: 26.638 distance: 85 - 87: 14.286 distance: 88 - 89: 21.508 distance: 89 - 90: 38.994 distance: 90 - 91: 18.328 distance: 90 - 92: 39.677 distance: 92 - 93: 26.608 distance: 93 - 94: 15.813 distance: 93 - 96: 20.296 distance: 94 - 95: 7.897 distance: 94 - 101: 17.203 distance: 96 - 97: 17.311 distance: 97 - 98: 8.688 distance: 98 - 99: 10.178 distance: 99 - 100: 14.109 distance: 101 - 102: 6.974 distance: 102 - 103: 4.368 distance: 102 - 105: 13.021 distance: 103 - 104: 6.055 distance: 103 - 110: 4.321 distance: 105 - 106: 7.152 distance: 106 - 107: 23.352 distance: 107 - 108: 20.455 distance: 108 - 109: 22.267 distance: 110 - 111: 6.346 distance: 111 - 112: 6.389 distance: 111 - 114: 5.945 distance: 112 - 113: 9.051 distance: 112 - 118: 5.990 distance: 114 - 115: 8.788 distance: 114 - 116: 15.358 distance: 115 - 117: 20.728 distance: 118 - 119: 5.128 distance: 119 - 120: 4.931 distance: 119 - 122: 10.304 distance: 120 - 121: 4.022 distance: 120 - 123: 7.960