Starting phenix.real_space_refine on Sun Jul 5 11:47:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c28_45137/07_2026/9c28_45137.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c28_45137/07_2026/9c28_45137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c28_45137/07_2026/9c28_45137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c28_45137/07_2026/9c28_45137.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c28_45137/07_2026/9c28_45137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c28_45137/07_2026/9c28_45137.map" } resolution = 3.12 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= 0.001 sd= 0.029 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: 5 Type Number sf(0) Gaussians Mn 20 7.51 5 S 240 5.16 5 C 17680 2.51 5 N 5030 2.21 5 O 5040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28010 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2799 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 23, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 2.64, per 1000 atoms: 0.09 Number of scatterers: 28010 At special positions: 0 Unit cell: (132.87, 129.78, 104.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 20 24.99 S 240 16.00 O 5040 8.00 N 5030 7.00 C 17680 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: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6680 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 37.0% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.861A pdb=" N LYS A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 65 through 68 removed outlier: 4.079A pdb=" N PHE A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 233 removed outlier: 4.166A pdb=" N GLY A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.562A pdb=" N ILE A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.861A pdb=" N LYS B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 65 through 68 removed outlier: 4.079A pdb=" N PHE B 68 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 233 removed outlier: 4.166A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.562A pdb=" N ILE B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.861A pdb=" N LYS C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 65 through 68 removed outlier: 4.078A pdb=" N PHE C 68 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 233 removed outlier: 4.166A pdb=" N GLY C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 266 through 280 removed outlier: 3.563A pdb=" N ILE C 270 " --> pdb=" O GLY C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 295 through 299 Processing helix chain 'C' and resid 326 through 333 Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 10 through 19 removed outlier: 3.861A pdb=" N LYS D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 65 through 68 removed outlier: 4.079A pdb=" N PHE D 68 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.612A pdb=" N VAL D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 233 removed outlier: 4.166A pdb=" N GLY D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 266 through 280 removed outlier: 3.562A pdb=" N ILE D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 347 through 360 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 10 through 19 removed outlier: 3.861A pdb=" N LYS E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 65 through 68 removed outlier: 4.079A pdb=" N PHE E 68 " --> pdb=" O SER E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 233 removed outlier: 4.166A pdb=" N GLY E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.562A pdb=" N ILE E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 295 through 299 Processing helix chain 'E' and resid 326 through 333 Processing helix chain 'E' and resid 347 through 360 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.862A pdb=" N LYS F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 65 through 68 removed outlier: 4.079A pdb=" N PHE F 68 " --> pdb=" O SER F 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 65 through 68' Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 126 through 128 No H-bonds generated for 'chain 'F' and resid 126 through 128' Processing helix chain 'F' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 233 removed outlier: 4.166A pdb=" N GLY F 215 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 266 through 280 removed outlier: 3.562A pdb=" N ILE F 270 " --> pdb=" O GLY F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 326 through 333 Processing helix chain 'F' and resid 347 through 360 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 10 through 19 removed outlier: 3.861A pdb=" N LYS G 14 " --> pdb=" O ASN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 65 through 68 removed outlier: 4.078A pdb=" N PHE G 68 " --> pdb=" O SER G 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 65 through 68' Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 126 through 128 No H-bonds generated for 'chain 'G' and resid 126 through 128' Processing helix chain 'G' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL G 176 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 233 removed outlier: 4.165A pdb=" N GLY G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 266 through 280 removed outlier: 3.562A pdb=" N ILE G 270 " --> pdb=" O GLY G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 287 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'H' and resid 4 through 9 Processing helix chain 'H' and resid 10 through 19 removed outlier: 3.861A pdb=" N LYS H 14 " --> pdb=" O ASN H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 65 through 68 removed outlier: 4.078A pdb=" N PHE H 68 " --> pdb=" O SER H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 128 No H-bonds generated for 'chain 'H' and resid 126 through 128' Processing helix chain 'H' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL H 176 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 233 removed outlier: 4.166A pdb=" N GLY H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 266 through 280 removed outlier: 3.562A pdb=" N ILE H 270 " --> pdb=" O GLY H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 287 Processing helix chain 'H' and resid 295 through 299 Processing helix chain 'H' and resid 326 through 333 Processing helix chain 'H' and resid 347 through 360 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 10 through 19 removed outlier: 3.862A pdb=" N LYS I 14 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 65 through 68 removed outlier: 4.079A pdb=" N PHE I 68 " --> pdb=" O SER I 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 65 through 68' Processing helix chain 'I' and resid 113 through 125 Processing helix chain 'I' and resid 126 through 128 No H-bonds generated for 'chain 'I' and resid 126 through 128' Processing helix chain 'I' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL I 176 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 233 removed outlier: 4.166A pdb=" N GLY I 215 " --> pdb=" O GLY I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 263 Processing helix chain 'I' and resid 266 through 280 removed outlier: 3.562A pdb=" N ILE I 270 " --> pdb=" O GLY I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 287 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 326 through 333 Processing helix chain 'I' and resid 347 through 360 Processing helix chain 'J' and resid 4 through 9 Processing helix chain 'J' and resid 10 through 19 removed outlier: 3.861A pdb=" N LYS J 14 " --> pdb=" O ASN J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 65 through 68 removed outlier: 4.079A pdb=" N PHE J 68 " --> pdb=" O SER J 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 65 through 68' Processing helix chain 'J' and resid 113 through 125 Processing helix chain 'J' and resid 126 through 128 No H-bonds generated for 'chain 'J' and resid 126 through 128' Processing helix chain 'J' and resid 172 through 187 removed outlier: 3.613A pdb=" N VAL J 176 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 233 removed outlier: 4.165A pdb=" N GLY J 215 " --> pdb=" O GLY J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 266 through 280 removed outlier: 3.563A pdb=" N ILE J 270 " --> pdb=" O GLY J 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 287 Processing helix chain 'J' and resid 295 through 299 Processing helix chain 'J' and resid 326 through 333 Processing helix chain 'J' and resid 347 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 5.441A pdb=" N LEU A 79 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE A 102 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU A 100 " --> pdb=" O PRO A 81 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN A 27 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL A 97 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET A 29 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS A 99 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 31 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 101 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL A 33 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N CYS A 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA E 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR E 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN E 205 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR E 193 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU E 203 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA E 195 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN E 201 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET E 133 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 209 through 210 removed outlier: 3.788A pdb=" N HIS E 253 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY E 315 " --> pdb=" O ILE E 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 209 through 210 removed outlier: 3.788A pdb=" N HIS A 253 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 315 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 237 removed outlier: 3.544A pdb=" N MET A 133 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN A 201 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA A 195 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A 203 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR A 193 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN A 205 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR A 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ALA A 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N CYS B 42 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN B 27 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 97 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N MET B 29 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS B 99 " --> pdb=" O MET B 29 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 31 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 101 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL B 33 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU B 100 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE B 102 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU B 79 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 209 through 210 removed outlier: 3.789A pdb=" N HIS B 253 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY B 315 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 235 through 237 removed outlier: 3.544A pdb=" N MET B 133 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN B 201 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA B 195 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU B 203 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 193 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN B 205 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR B 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA B 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS C 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN C 27 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL C 97 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET C 29 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS C 99 " --> pdb=" O MET C 29 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE C 31 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 101 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL C 33 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU C 100 " --> pdb=" O PRO C 81 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE C 102 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LEU C 79 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 209 through 210 removed outlier: 3.788A pdb=" N HIS C 253 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY C 315 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 237 removed outlier: 3.545A pdb=" N MET C 133 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN C 201 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA C 195 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU C 203 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR C 193 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN C 205 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA C 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N CYS D 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN D 27 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL D 97 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET D 29 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS D 99 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE D 31 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL D 101 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL D 33 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU D 100 " --> pdb=" O PRO D 81 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE D 102 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU D 79 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 209 through 210 removed outlier: 3.789A pdb=" N HIS D 253 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY D 315 " --> pdb=" O ILE D 325 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 235 through 237 removed outlier: 3.544A pdb=" N MET D 133 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN D 201 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA D 195 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU D 203 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR D 193 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN D 205 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR D 191 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA D 195 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N CYS E 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN E 27 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL E 97 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET E 29 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS E 99 " --> pdb=" O MET E 29 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE E 31 " --> pdb=" O CYS E 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL E 101 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL E 33 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU E 100 " --> pdb=" O PRO E 81 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE E 102 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU E 79 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 60 through 63 removed outlier: 5.442A pdb=" N LEU F 79 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE F 102 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU F 100 " --> pdb=" O PRO F 81 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN F 27 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL F 97 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET F 29 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS F 99 " --> pdb=" O MET F 29 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE F 31 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL F 101 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL F 33 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N CYS F 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA J 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR J 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN J 205 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR J 193 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU J 203 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA J 195 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN J 201 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET J 133 " --> pdb=" O ILE J 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 209 through 210 removed outlier: 3.788A pdb=" N HIS J 253 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY J 315 " --> pdb=" O ILE J 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 209 through 210 removed outlier: 3.788A pdb=" N HIS F 253 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY F 315 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 237 removed outlier: 3.544A pdb=" N MET F 133 " --> pdb=" O ILE F 206 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN F 201 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA F 195 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU F 203 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR F 193 " --> pdb=" O GLU F 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN F 205 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR F 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA F 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N CYS G 42 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN G 27 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL G 97 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N MET G 29 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS G 99 " --> pdb=" O MET G 29 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE G 31 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL G 101 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL G 33 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU G 100 " --> pdb=" O PRO G 81 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE G 102 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU G 79 " --> pdb=" O PHE G 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 209 through 210 removed outlier: 3.788A pdb=" N HIS G 253 " --> pdb=" O GLU G 134 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY G 315 " --> pdb=" O ILE G 325 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 235 through 237 removed outlier: 3.545A pdb=" N MET G 133 " --> pdb=" O ILE G 206 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN G 201 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA G 195 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU G 203 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR G 193 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN G 205 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR G 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA G 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS H 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN H 27 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL H 97 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N MET H 29 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS H 99 " --> pdb=" O MET H 29 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE H 31 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL H 101 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU H 100 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE H 102 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU H 79 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 209 through 210 removed outlier: 3.788A pdb=" N HIS H 253 " --> pdb=" O GLU H 134 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY H 315 " --> pdb=" O ILE H 325 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 235 through 237 removed outlier: 3.545A pdb=" N MET H 133 " --> pdb=" O ILE H 206 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN H 201 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA H 195 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU H 203 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR H 193 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN H 205 " --> pdb=" O THR H 191 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR H 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA H 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N CYS I 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN I 27 " --> pdb=" O LYS I 95 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL I 97 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N MET I 29 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS I 99 " --> pdb=" O MET I 29 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE I 31 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL I 101 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL I 33 " --> pdb=" O VAL I 101 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU I 100 " --> pdb=" O PRO I 81 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE I 102 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU I 79 " --> pdb=" O PHE I 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 209 through 210 removed outlier: 3.788A pdb=" N HIS I 253 " --> pdb=" O GLU I 134 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N GLY I 315 " --> pdb=" O ILE I 325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 235 through 237 removed outlier: 3.545A pdb=" N MET I 133 " --> pdb=" O ILE I 206 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN I 201 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ALA I 195 " --> pdb=" O GLN I 201 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU I 203 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR I 193 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN I 205 " --> pdb=" O THR I 191 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N THR I 191 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ALA I 195 " --> pdb=" O CYS J 42 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N CYS J 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN J 27 " --> pdb=" O LYS J 95 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL J 97 " --> pdb=" O GLN J 27 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET J 29 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS J 99 " --> pdb=" O MET J 29 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE J 31 " --> pdb=" O CYS J 99 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL J 101 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL J 33 " --> pdb=" O VAL J 101 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU J 100 " --> pdb=" O PRO J 81 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE J 102 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU J 79 " --> pdb=" O PHE J 102 " (cutoff:3.500A) 1220 hydrogen bonds defined for protein. 3270 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9360 1.35 - 1.46: 6890 1.46 - 1.58: 12150 1.58 - 1.70: 0 1.70 - 1.81: 360 Bond restraints: 28760 Sorted by residual: bond pdb=" CB MET C 121 " pdb=" CG MET C 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.53e-01 bond pdb=" CB MET E 121 " pdb=" CG MET E 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.43e-01 bond pdb=" CB MET A 121 " pdb=" CG MET A 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.43e-01 bond pdb=" CB MET F 121 " pdb=" CG MET F 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.43e-01 bond pdb=" CB MET H 121 " pdb=" CG MET H 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.41e-01 ... (remaining 28755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 38033 1.21 - 2.42: 666 2.42 - 3.63: 281 3.63 - 4.84: 50 4.84 - 6.05: 10 Bond angle restraints: 39040 Sorted by residual: angle pdb=" N ARG J 341 " pdb=" CA ARG J 341 " pdb=" C ARG J 341 " ideal model delta sigma weight residual 109.81 114.44 -4.63 2.21e+00 2.05e-01 4.40e+00 angle pdb=" N ARG B 341 " pdb=" CA ARG B 341 " pdb=" C ARG B 341 " ideal model delta sigma weight residual 109.81 114.42 -4.61 2.21e+00 2.05e-01 4.34e+00 angle pdb=" N ARG C 341 " pdb=" CA ARG C 341 " pdb=" C ARG C 341 " ideal model delta sigma weight residual 109.81 114.41 -4.60 2.21e+00 2.05e-01 4.33e+00 angle pdb=" N ARG H 341 " pdb=" CA ARG H 341 " pdb=" C ARG H 341 " ideal model delta sigma weight residual 109.81 114.41 -4.60 2.21e+00 2.05e-01 4.33e+00 angle pdb=" N ARG F 341 " pdb=" CA ARG F 341 " pdb=" C ARG F 341 " ideal model delta sigma weight residual 109.81 114.41 -4.60 2.21e+00 2.05e-01 4.32e+00 ... (remaining 39035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 15098 17.72 - 35.43: 1392 35.43 - 53.15: 350 53.15 - 70.86: 60 70.86 - 88.58: 40 Dihedral angle restraints: 16940 sinusoidal: 6450 harmonic: 10490 Sorted by residual: dihedral pdb=" CG ARG G 340 " pdb=" CD ARG G 340 " pdb=" NE ARG G 340 " pdb=" CZ ARG G 340 " ideal model delta sinusoidal sigma weight residual 180.00 -136.78 -43.22 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG B 340 " pdb=" CD ARG B 340 " pdb=" NE ARG B 340 " pdb=" CZ ARG B 340 " ideal model delta sinusoidal sigma weight residual -180.00 -136.78 -43.22 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG J 340 " pdb=" CD ARG J 340 " pdb=" NE ARG J 340 " pdb=" CZ ARG J 340 " ideal model delta sinusoidal sigma weight residual -180.00 -136.78 -43.22 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 16937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2261 0.027 - 0.053: 1149 0.053 - 0.080: 383 0.080 - 0.107: 197 0.107 - 0.133: 60 Chirality restraints: 4050 Sorted by residual: chirality pdb=" CA ILE H 325 " pdb=" N ILE H 325 " pdb=" C ILE H 325 " pdb=" CB ILE H 325 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE G 325 " pdb=" N ILE G 325 " pdb=" C ILE G 325 " pdb=" CB ILE G 325 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 325 " pdb=" N ILE A 325 " pdb=" C ILE A 325 " pdb=" CB ILE A 325 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 4047 not shown) Planarity restraints: 5170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 159 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO I 160 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 160 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 159 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO D 160 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 159 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO J 160 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 160 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 160 " -0.032 5.00e-02 4.00e+02 ... (remaining 5167 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6602 2.78 - 3.31: 26093 3.31 - 3.84: 50179 3.84 - 4.37: 59444 4.37 - 4.90: 103636 Nonbonded interactions: 245954 Sorted by model distance: nonbonded pdb=" OD1 ASP D 216 " pdb=" OH TYR D 349 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP E 216 " pdb=" OH TYR E 349 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP B 216 " pdb=" OH TYR B 349 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP C 216 " pdb=" OH TYR C 349 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP F 216 " pdb=" OH TYR F 349 " model vdw 2.255 3.040 ... (remaining 245949 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: 0.11 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' } 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: 0.950 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: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.700 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.002 0.024 28760 Z= 0.107 Angle : 0.482 6.054 39040 Z= 0.251 Chirality : 0.040 0.133 4050 Planarity : 0.004 0.058 5170 Dihedral : 15.319 88.575 10260 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.04 % Allowed : 16.46 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.15), residues: 3640 helix: 2.00 (0.16), residues: 1070 sheet: -0.48 (0.17), residues: 850 loop : 0.58 (0.17), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 262 TYR 0.004 0.001 TYR C 137 PHE 0.007 0.001 PHE B 204 TRP 0.004 0.001 TRP I 202 HIS 0.002 0.000 HIS G 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (28760) covalent geometry : angle 0.48163 / 0.25 (39040) hydrogen bonds : bond 0.18638 / 12.41 ( 1220) hydrogen bonds : angle 6.50578 / 4.79 ( 3270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 316 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 267 LEU cc_start: 0.8302 (mt) cc_final: 0.7236 (mt) REVERT: D 17 TYR cc_start: 0.8704 (m-80) cc_final: 0.8377 (m-80) REVERT: D 161 TYR cc_start: 0.8975 (m-80) cc_final: 0.8677 (m-80) REVERT: D 213 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7403 (mtm110) REVERT: D 267 LEU cc_start: 0.8240 (mt) cc_final: 0.7199 (mt) REVERT: E 18 MET cc_start: 0.8875 (mmm) cc_final: 0.8673 (mmm) REVERT: E 213 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7613 (mtp-110) REVERT: H 267 LEU cc_start: 0.8301 (mt) cc_final: 0.7234 (mt) REVERT: I 17 TYR cc_start: 0.8703 (m-80) cc_final: 0.8378 (m-80) REVERT: I 161 TYR cc_start: 0.8975 (m-80) cc_final: 0.8677 (m-80) REVERT: I 213 ARG cc_start: 0.7962 (mtp85) cc_final: 0.7404 (mtm110) REVERT: I 267 LEU cc_start: 0.8240 (mt) cc_final: 0.7198 (mt) REVERT: J 213 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7612 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 317 average time/residue: 0.1823 time to fit residues: 92.4049 Evaluate side-chains 272 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0970 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 19 ASN A 152 ASN B 15 GLN B 19 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN C 19 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 19 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN E 19 ASN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 19 ASN F 152 ASN G 15 GLN G 19 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN H 19 ASN ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 19 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN J 19 ASN ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.103904 restraints weight = 36077.374| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.34 r_work: 0.3143 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 28760 Z= 0.252 Angle : 0.568 5.224 39040 Z= 0.300 Chirality : 0.045 0.140 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.957 18.993 4030 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.53 % Allowed : 13.54 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3640 helix: 1.69 (0.16), residues: 1070 sheet: -0.50 (0.18), residues: 850 loop : 0.48 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 41 TYR 0.010 0.001 TYR C 137 PHE 0.012 0.002 PHE H 98 TRP 0.006 0.001 TRP D 130 HIS 0.004 0.001 HIS C 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.25 (28760) covalent geometry : angle 0.56752 / 0.30 (39040) hydrogen bonds : bond 0.04810 / 3.18 ( 1220) hydrogen bonds : angle 5.46761 / 4.00 ( 3270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 276 time to evaluate : 0.922 Fit side-chains REVERT: B 213 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7517 (mtm180) REVERT: C 213 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7896 (mtm180) REVERT: C 289 ASP cc_start: 0.6994 (p0) cc_final: 0.6667 (p0) REVERT: D 17 TYR cc_start: 0.8835 (m-80) cc_final: 0.8570 (m-80) REVERT: D 134 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8717 (mt-10) REVERT: D 161 TYR cc_start: 0.9155 (m-80) cc_final: 0.8855 (m-80) REVERT: D 213 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7552 (mtm110) REVERT: D 267 LEU cc_start: 0.8031 (mt) cc_final: 0.7548 (mt) REVERT: D 271 GLU cc_start: 0.8506 (mp0) cc_final: 0.8004 (mp0) REVERT: E 213 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7779 (mtp-110) REVERT: G 213 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7514 (mtm180) REVERT: H 213 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7893 (mtm180) REVERT: H 289 ASP cc_start: 0.7009 (p0) cc_final: 0.6681 (p0) REVERT: I 17 TYR cc_start: 0.8839 (m-80) cc_final: 0.8572 (m-80) REVERT: I 134 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8710 (mt-10) REVERT: I 161 TYR cc_start: 0.9145 (m-80) cc_final: 0.8845 (m-80) REVERT: I 213 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7550 (mtm110) REVERT: I 267 LEU cc_start: 0.8029 (mt) cc_final: 0.7538 (mt) REVERT: I 271 GLU cc_start: 0.8493 (mp0) cc_final: 0.7991 (mp0) REVERT: J 213 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7781 (mtp-110) outliers start: 70 outliers final: 32 residues processed: 310 average time/residue: 0.1835 time to fit residues: 89.6067 Evaluate side-chains 292 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 329 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 345 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104206 restraints weight = 36358.705| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.34 r_work: 0.3130 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 28760 Z= 0.273 Angle : 0.571 5.829 39040 Z= 0.297 Chirality : 0.045 0.145 4050 Planarity : 0.004 0.055 5170 Dihedral : 4.130 21.898 4030 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.67 % Allowed : 13.72 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3640 helix: 1.59 (0.16), residues: 1070 sheet: -0.56 (0.19), residues: 860 loop : 0.36 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 324 TYR 0.010 0.001 TYR D 137 PHE 0.011 0.002 PHE C 68 TRP 0.006 0.001 TRP J 149 HIS 0.004 0.001 HIS I 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.27 (28760) covalent geometry : angle 0.57100 / 0.30 (39040) hydrogen bonds : bond 0.04589 / 3.03 ( 1220) hydrogen bonds : angle 5.32766 / 3.89 ( 3270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 259 time to evaluate : 1.173 Fit side-chains REVERT: A 133 MET cc_start: 0.9142 (mtp) cc_final: 0.8920 (mtp) REVERT: B 213 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7375 (mtm110) REVERT: B 267 LEU cc_start: 0.8242 (mt) cc_final: 0.7242 (mt) REVERT: C 213 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7797 (mtm180) REVERT: D 134 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8773 (mt-10) REVERT: D 213 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7492 (mtm110) REVERT: D 267 LEU cc_start: 0.8182 (mt) cc_final: 0.7189 (mt) REVERT: D 271 GLU cc_start: 0.8500 (mp0) cc_final: 0.8229 (mp0) REVERT: E 134 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8915 (mt-10) REVERT: E 213 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7780 (mtp-110) REVERT: E 319 ARG cc_start: 0.8450 (mmt180) cc_final: 0.8244 (mmt180) REVERT: F 133 MET cc_start: 0.9146 (mtp) cc_final: 0.8917 (mtp) REVERT: G 213 ARG cc_start: 0.7999 (mtp85) cc_final: 0.7344 (mtm110) REVERT: G 214 MET cc_start: 0.8670 (tpp) cc_final: 0.7901 (tpp) REVERT: G 267 LEU cc_start: 0.8231 (mt) cc_final: 0.7236 (mt) REVERT: H 213 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7784 (mtm180) REVERT: I 134 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8782 (mt-10) REVERT: I 213 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7488 (mtm110) REVERT: I 267 LEU cc_start: 0.8186 (mt) cc_final: 0.7179 (mt) REVERT: I 271 GLU cc_start: 0.8488 (mp0) cc_final: 0.8218 (mp0) REVERT: J 134 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8910 (mt-10) REVERT: J 213 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7772 (mtp-110) REVERT: J 319 ARG cc_start: 0.8443 (mmt180) cc_final: 0.8235 (mmt180) outliers start: 74 outliers final: 43 residues processed: 310 average time/residue: 0.2071 time to fit residues: 101.5428 Evaluate side-chains 292 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 309 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 18 optimal weight: 0.6980 chunk 213 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 317 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 330 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106261 restraints weight = 35438.002| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.34 r_work: 0.3175 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28760 Z= 0.143 Angle : 0.505 5.818 39040 Z= 0.263 Chirality : 0.042 0.151 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.877 19.204 4030 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.74 % Allowed : 13.25 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 3640 helix: 1.66 (0.16), residues: 1070 sheet: -0.47 (0.19), residues: 820 loop : 0.42 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 262 TYR 0.007 0.001 TYR E 137 PHE 0.009 0.001 PHE D 337 TRP 0.003 0.001 TRP B 247 HIS 0.002 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (28760) covalent geometry : angle 0.50452 / 0.26 (39040) hydrogen bonds : bond 0.03854 / 2.54 ( 1220) hydrogen bonds : angle 5.14931 / 3.75 ( 3270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 285 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 213 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7751 (mtm180) REVERT: D 17 TYR cc_start: 0.8762 (m-80) cc_final: 0.8471 (m-80) REVERT: D 77 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8086 (mtt) REVERT: D 134 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8849 (mt-10) REVERT: D 161 TYR cc_start: 0.9097 (m-80) cc_final: 0.8843 (m-80) REVERT: D 213 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7403 (mtm110) REVERT: E 134 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8913 (mt-10) REVERT: E 213 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7720 (mtp-110) REVERT: E 319 ARG cc_start: 0.8435 (mmt180) cc_final: 0.8231 (mmt180) REVERT: H 213 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7752 (mtm180) REVERT: I 17 TYR cc_start: 0.8760 (m-80) cc_final: 0.8462 (m-80) REVERT: I 77 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8065 (mtt) REVERT: I 134 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8849 (mt-10) REVERT: I 161 TYR cc_start: 0.9091 (m-80) cc_final: 0.8837 (m-80) REVERT: I 213 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7400 (mtm110) REVERT: J 134 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8913 (mt-10) REVERT: J 213 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7717 (mtp-110) REVERT: J 319 ARG cc_start: 0.8419 (mmt180) cc_final: 0.8213 (mmt180) outliers start: 76 outliers final: 43 residues processed: 337 average time/residue: 0.1855 time to fit residues: 100.7693 Evaluate side-chains 293 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 219 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 241 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103037 restraints weight = 36031.605| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.33 r_work: 0.3130 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 28760 Z= 0.248 Angle : 0.558 6.451 39040 Z= 0.289 Chirality : 0.044 0.147 4050 Planarity : 0.004 0.053 5170 Dihedral : 4.080 21.644 4030 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 14.51 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.15), residues: 3640 helix: 1.50 (0.16), residues: 1070 sheet: -0.70 (0.19), residues: 860 loop : 0.35 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 227 TYR 0.010 0.001 TYR I 137 PHE 0.010 0.002 PHE H 68 TRP 0.005 0.001 TRP J 149 HIS 0.004 0.001 HIS I 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.25 (28760) covalent geometry : angle 0.55798 / 0.29 (39040) hydrogen bonds : bond 0.04312 / 2.85 ( 1220) hydrogen bonds : angle 5.19001 / 3.78 ( 3270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 255 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 LEU cc_start: 0.8224 (mt) cc_final: 0.7813 (mt) REVERT: D 77 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8101 (mtt) REVERT: D 134 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8876 (mt-10) REVERT: D 213 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7503 (mtm110) REVERT: E 134 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8914 (mt-10) REVERT: E 213 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7754 (mtp-110) REVERT: E 319 ARG cc_start: 0.8461 (mmt180) cc_final: 0.8256 (mmt180) REVERT: F 133 MET cc_start: 0.9115 (mtp) cc_final: 0.8863 (mtp) REVERT: G 267 LEU cc_start: 0.8227 (mt) cc_final: 0.7817 (mt) REVERT: I 77 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8096 (mtt) REVERT: I 134 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8884 (mt-10) REVERT: I 213 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7508 (mtm110) REVERT: J 134 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8925 (mt-10) REVERT: J 213 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7745 (mtp-110) REVERT: J 319 ARG cc_start: 0.8466 (mmt180) cc_final: 0.8255 (mmt180) outliers start: 69 outliers final: 46 residues processed: 302 average time/residue: 0.1910 time to fit residues: 92.8461 Evaluate side-chains 297 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 309 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 187 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 353 optimal weight: 10.0000 chunk 246 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.105945 restraints weight = 35591.280| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.30 r_work: 0.3166 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28760 Z= 0.156 Angle : 0.509 6.367 39040 Z= 0.263 Chirality : 0.042 0.159 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.897 19.914 4030 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.56 % Allowed : 14.80 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3640 helix: 1.62 (0.16), residues: 1070 sheet: -0.59 (0.19), residues: 820 loop : 0.38 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 324 TYR 0.007 0.001 TYR E 137 PHE 0.009 0.001 PHE A 223 TRP 0.003 0.001 TRP B 247 HIS 0.002 0.001 HIS G 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (28760) covalent geometry : angle 0.50905 / 0.26 (39040) hydrogen bonds : bond 0.03829 / 2.53 ( 1220) hydrogen bonds : angle 5.03155 / 3.66 ( 3270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 TYR cc_start: 0.8778 (m-80) cc_final: 0.8509 (m-80) REVERT: D 77 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8113 (mtt) REVERT: D 134 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8878 (mt-10) REVERT: D 161 TYR cc_start: 0.9139 (m-80) cc_final: 0.8824 (m-80) REVERT: D 213 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7551 (mtm110) REVERT: E 134 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8913 (mt-10) REVERT: E 213 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7804 (mtp-110) REVERT: E 319 ARG cc_start: 0.8501 (mmt180) cc_final: 0.8283 (mmt180) REVERT: I 17 TYR cc_start: 0.8778 (m-80) cc_final: 0.8501 (m-80) REVERT: I 77 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: I 134 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8891 (mt-10) REVERT: I 161 TYR cc_start: 0.9133 (m-80) cc_final: 0.8815 (m-80) REVERT: I 213 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7544 (mtm110) REVERT: J 134 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8923 (mt-10) REVERT: J 213 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7792 (mtp-110) REVERT: J 319 ARG cc_start: 0.8496 (mmt180) cc_final: 0.8278 (mmt180) outliers start: 71 outliers final: 48 residues processed: 321 average time/residue: 0.1888 time to fit residues: 97.5422 Evaluate side-chains 306 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 138 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 320 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 329 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102697 restraints weight = 35837.135| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.34 r_work: 0.3127 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 28760 Z= 0.246 Angle : 0.559 8.582 39040 Z= 0.287 Chirality : 0.044 0.151 4050 Planarity : 0.004 0.054 5170 Dihedral : 4.093 21.932 4030 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.64 % Allowed : 15.20 % Favored : 82.17 % 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 are not related in a simple way. whole: 0.51 (0.15), residues: 3640 helix: 1.50 (0.16), residues: 1070 sheet: -0.69 (0.19), residues: 820 loop : 0.29 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 227 TYR 0.010 0.001 TYR I 137 PHE 0.010 0.002 PHE B 223 TRP 0.005 0.001 TRP E 149 HIS 0.003 0.001 HIS E 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 (28760) covalent geometry : angle 0.55904 / 0.29 (39040) hydrogen bonds : bond 0.04237 / 2.80 ( 1220) hydrogen bonds : angle 5.09092 / 3.71 ( 3270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 253 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 213 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7400 (mtm110) REVERT: D 77 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8116 (mtt) REVERT: D 134 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8885 (mt-10) REVERT: D 213 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7620 (mtm110) REVERT: E 134 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8946 (mt-10) REVERT: E 213 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7895 (mtp-110) REVERT: F 175 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8499 (mp) REVERT: G 213 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7441 (mtm180) REVERT: I 77 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8109 (mtt) REVERT: I 134 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8900 (mt-10) REVERT: I 213 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7614 (mtm110) REVERT: J 134 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8952 (mt-10) REVERT: J 213 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7883 (mtp-110) outliers start: 73 outliers final: 54 residues processed: 303 average time/residue: 0.1937 time to fit residues: 94.0011 Evaluate side-chains 305 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 243 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 285 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 309 ILE Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 309 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 293 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108564 restraints weight = 35553.096| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.33 r_work: 0.3201 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28760 Z= 0.114 Angle : 0.485 6.791 39040 Z= 0.249 Chirality : 0.041 0.154 4050 Planarity : 0.004 0.058 5170 Dihedral : 3.747 18.274 4030 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.17 % Allowed : 15.88 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 3640 helix: 1.74 (0.16), residues: 1070 sheet: -0.50 (0.20), residues: 800 loop : 0.45 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 262 TYR 0.010 0.001 TYR G 349 PHE 0.009 0.001 PHE I 337 TRP 0.005 0.001 TRP D 130 HIS 0.003 0.001 HIS E 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (28760) covalent geometry : angle 0.48488 / 0.25 (39040) hydrogen bonds : bond 0.03448 / 2.27 ( 1220) hydrogen bonds : angle 4.87423 / 3.54 ( 3270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 292 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ILE cc_start: 0.9042 (mm) cc_final: 0.8828 (mt) REVERT: C 47 LEU cc_start: 0.8320 (tp) cc_final: 0.7968 (tp) REVERT: D 77 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8053 (mtt) REVERT: D 134 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8789 (mt-10) REVERT: D 161 TYR cc_start: 0.9074 (m-80) cc_final: 0.8781 (m-80) REVERT: D 213 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7437 (mtm110) REVERT: E 213 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7720 (mtp-110) REVERT: E 231 ASP cc_start: 0.8871 (m-30) cc_final: 0.8430 (m-30) REVERT: E 319 ARG cc_start: 0.8462 (mmt180) cc_final: 0.8232 (mmt180) REVERT: H 13 ILE cc_start: 0.9051 (mm) cc_final: 0.8843 (mt) REVERT: H 47 LEU cc_start: 0.8324 (tp) cc_final: 0.7955 (tp) REVERT: I 77 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8017 (mtt) REVERT: I 134 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8802 (mt-10) REVERT: I 161 TYR cc_start: 0.9069 (m-80) cc_final: 0.8771 (m-80) REVERT: I 213 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7407 (mtm110) REVERT: J 17 TYR cc_start: 0.8778 (m-80) cc_final: 0.8484 (m-80) REVERT: J 213 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7715 (mtp-110) REVERT: J 231 ASP cc_start: 0.8878 (m-30) cc_final: 0.8419 (m-30) REVERT: J 319 ARG cc_start: 0.8454 (mmt180) cc_final: 0.8226 (mmt180) outliers start: 60 outliers final: 47 residues processed: 333 average time/residue: 0.1655 time to fit residues: 90.8250 Evaluate side-chains 309 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 171 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 191 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 216 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109419 restraints weight = 35475.511| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.33 r_work: 0.3225 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 28760 Z= 0.111 Angle : 0.494 7.779 39040 Z= 0.251 Chirality : 0.041 0.151 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.678 16.745 4030 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.99 % Allowed : 15.88 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.15), residues: 3640 helix: 1.81 (0.16), residues: 1070 sheet: -0.49 (0.20), residues: 800 loop : 0.53 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 227 TYR 0.010 0.001 TYR B 349 PHE 0.010 0.001 PHE I 337 TRP 0.004 0.001 TRP F 130 HIS 0.002 0.001 HIS F 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (28760) covalent geometry : angle 0.49437 / 0.25 (39040) hydrogen bonds : bond 0.03410 / 2.25 ( 1220) hydrogen bonds : angle 4.78854 / 3.48 ( 3270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 268 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9179 (mtp) cc_final: 0.8944 (mtt) REVERT: A 175 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8685 (mp) REVERT: C 47 LEU cc_start: 0.8291 (tp) cc_final: 0.7951 (tp) REVERT: C 261 MET cc_start: 0.8693 (ttm) cc_final: 0.8451 (ttm) REVERT: C 271 GLU cc_start: 0.8601 (mp0) cc_final: 0.8389 (mp0) REVERT: D 77 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8051 (mtt) REVERT: D 134 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8772 (mt-10) REVERT: D 161 TYR cc_start: 0.9048 (m-80) cc_final: 0.8689 (m-80) REVERT: D 213 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7467 (mtm110) REVERT: E 17 TYR cc_start: 0.8745 (m-80) cc_final: 0.8330 (m-80) REVERT: E 213 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7715 (mtp-110) REVERT: E 231 ASP cc_start: 0.8887 (m-30) cc_final: 0.8428 (m-30) REVERT: E 319 ARG cc_start: 0.8497 (mmt180) cc_final: 0.8252 (mmt180) REVERT: F 140 MET cc_start: 0.9174 (mtp) cc_final: 0.8937 (mtt) REVERT: F 175 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8676 (mp) REVERT: G 140 MET cc_start: 0.9136 (mtp) cc_final: 0.8912 (mtt) REVERT: H 47 LEU cc_start: 0.8299 (tp) cc_final: 0.7959 (tp) REVERT: H 261 MET cc_start: 0.8719 (ttm) cc_final: 0.8455 (ttm) REVERT: H 271 GLU cc_start: 0.8592 (mp0) cc_final: 0.8390 (mp0) REVERT: I 77 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8014 (mtt) REVERT: I 134 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8791 (mt-10) REVERT: I 161 TYR cc_start: 0.9034 (m-80) cc_final: 0.8754 (m-80) REVERT: I 213 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7472 (mtm110) REVERT: J 17 TYR cc_start: 0.8828 (m-80) cc_final: 0.8571 (m-80) REVERT: J 213 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7707 (mtp-110) REVERT: J 231 ASP cc_start: 0.8879 (m-30) cc_final: 0.8421 (m-30) REVERT: J 319 ARG cc_start: 0.8490 (mmt180) cc_final: 0.8245 (mmt180) outliers start: 55 outliers final: 47 residues processed: 309 average time/residue: 0.1867 time to fit residues: 93.7825 Evaluate side-chains 311 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 258 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 150 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 178 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105158 restraints weight = 35620.643| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.31 r_work: 0.3168 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 28760 Z= 0.201 Angle : 0.545 8.259 39040 Z= 0.277 Chirality : 0.043 0.153 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.903 19.299 4030 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.09 % Allowed : 15.92 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 3640 helix: 1.64 (0.16), residues: 1070 sheet: -0.64 (0.19), residues: 850 loop : 0.45 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 341 TYR 0.010 0.001 TYR G 349 PHE 0.011 0.002 PHE H 223 TRP 0.005 0.001 TRP J 149 HIS 0.003 0.001 HIS I 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (28760) covalent geometry : angle 0.54453 / 0.28 (39040) hydrogen bonds : bond 0.03956 / 2.61 ( 1220) hydrogen bonds : angle 4.91403 / 3.57 ( 3270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 255 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9181 (mtp) cc_final: 0.8962 (mtt) REVERT: A 175 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8546 (mp) REVERT: B 140 MET cc_start: 0.9227 (mtp) cc_final: 0.9026 (mtt) REVERT: C 47 LEU cc_start: 0.8350 (tp) cc_final: 0.7985 (tp) REVERT: D 77 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: D 134 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: D 161 TYR cc_start: 0.9163 (m-80) cc_final: 0.8855 (m-80) REVERT: D 213 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7580 (mtm110) REVERT: E 213 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7783 (mtp-110) REVERT: E 214 MET cc_start: 0.8662 (tpp) cc_final: 0.8451 (tpt) REVERT: F 140 MET cc_start: 0.9182 (mtp) cc_final: 0.8964 (mtt) REVERT: F 175 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8537 (mp) REVERT: G 140 MET cc_start: 0.9238 (mtp) cc_final: 0.8778 (mtt) REVERT: H 261 MET cc_start: 0.8562 (ttm) cc_final: 0.8335 (ttm) REVERT: I 77 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8051 (mtt) REVERT: I 134 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8803 (mt-10) REVERT: I 161 TYR cc_start: 0.9152 (m-80) cc_final: 0.8831 (m-80) REVERT: I 213 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7573 (mtm110) REVERT: J 213 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7774 (mtp-110) REVERT: J 214 MET cc_start: 0.8667 (tpp) cc_final: 0.8453 (tpt) outliers start: 58 outliers final: 48 residues processed: 297 average time/residue: 0.1903 time to fit residues: 90.8650 Evaluate side-chains 300 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 175 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 328 ILE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 27 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 328 optimal weight: 7.9990 chunk 226 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.138706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107123 restraints weight = 35485.465| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.30 r_work: 0.3185 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28760 Z= 0.149 Angle : 0.515 8.188 39040 Z= 0.263 Chirality : 0.042 0.163 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.832 18.698 4030 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 16.28 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 3640 helix: 1.63 (0.16), residues: 1070 sheet: -0.51 (0.18), residues: 910 loop : 0.52 (0.17), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 41 TYR 0.011 0.001 TYR G 349 PHE 0.009 0.001 PHE A 223 TRP 0.004 0.001 TRP F 130 HIS 0.002 0.001 HIS J 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (28760) covalent geometry : angle 0.51509 / 0.26 (39040) hydrogen bonds : bond 0.03704 / 2.44 ( 1220) hydrogen bonds : angle 4.88766 / 3.55 ( 3270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6323.73 seconds wall clock time: 109 minutes 33.48 seconds (6573.48 seconds total)