Starting phenix.real_space_refine on Mon Aug 25 11:42:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c28_45137/08_2025/9c28_45137.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c28_45137/08_2025/9c28_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c28_45137/08_2025/9c28_45137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c28_45137/08_2025/9c28_45137.map" model { file = "/net/cci-nas-00/data/ceres_data/9c28_45137/08_2025/9c28_45137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c28_45137/08_2025/9c28_45137.cif" } 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-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 2.97, per 1000 atoms: 0.11 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: 1.81 Conformation dependent library (CDL) restraints added in 954.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.99 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: 5.74 Time building geometry restraints manager: 2.38 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.130 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.540 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 aren 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 covalent geometry : bond 0.00231 (28760) covalent geometry : angle 0.48163 (39040) hydrogen bonds : bond 0.18638 ( 1220) hydrogen bonds : angle 6.50578 ( 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 : 1.041 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: 0.8703 (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: 0.7402 (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: 0.8005 (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: 0.1613 time to fit residues: 81.4785 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 : 1.024 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3703 r_free = 0.3703 target = 0.136157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103830 restraints weight = 35966.160| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.33 r_work: 0.3144 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1117 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= 0.254 Angle : 0.572 5.219 39040 Z= 0.302 Chirality : 0.045 0.141 4050 Planarity : 0.004 0.056 5170 Dihedral : 4.003 19.248 4030 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.56 % Allowed : 13.50 % 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 aren not related in a simple way. whole: 0.77 (0.15), residues: 3640 helix: 1.68 (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 E 41 TYR 0.010 0.001 TYR C 137 PHE 0.011 0.002 PHE I 98 TRP 0.006 0.001 TRP I 130 HIS 0.004 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00608 (28760) covalent geometry : angle 0.57188 (39040) hydrogen bonds : bond 0.04803 ( 1220) hydrogen bonds : angle 5.43845 ( 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 340 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 269 time to evaluate : 1.043 Fit side-chains REVERT: B 213 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7446 (mtm180) REVERT: C 213 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7828 (mtm180) REVERT: C 289 ASP cc_start: 0.6980 (p0) cc_final: 0.6646 (p0) REVERT: D 134 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8687 (mt-10) REVERT: D 161 TYR cc_start: 0.9148 (m-80) cc_final: 0.8854 (m-80) REVERT: D 213 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7482 (mtm110) REVERT: E 213 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7788 (mtp-110) REVERT: G 213 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7412 (mtm180) REVERT: H 213 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7820 (mtm180) REVERT: I 134 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8684 (mt-10) REVERT: I 161 TYR cc_start: 0.9140 (m-80) cc_final: 0.8846 (m-80) REVERT: I 213 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7506 (mtm110) REVERT: J 213 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7777 (mtp-110) outliers start: 71 outliers final: 32 residues processed: 304 average time/residue: 0.1662 time to fit residues: 78.7318 Evaluate side-chains 291 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 257 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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: 5.9990 chunk 158 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 345 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 266 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.135972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103542 restraints weight = 35971.788| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.35 r_work: 0.3142 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 28760 Z= 0.235 Angle : 0.546 5.621 39040 Z= 0.284 Chirality : 0.044 0.139 4050 Planarity : 0.004 0.054 5170 Dihedral : 4.040 20.889 4030 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.42 % Allowed : 13.72 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.15), residues: 3640 helix: 1.62 (0.16), residues: 1070 sheet: -0.54 (0.19), residues: 860 loop : 0.42 (0.17), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 324 TYR 0.009 0.001 TYR C 17 PHE 0.010 0.002 PHE C 68 TRP 0.004 0.001 TRP J 149 HIS 0.004 0.001 HIS I 217 Details of bonding type rmsd covalent geometry : bond 0.00563 (28760) covalent geometry : angle 0.54562 (39040) hydrogen bonds : bond 0.04392 ( 1220) hydrogen bonds : angle 5.25481 ( 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 332 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 265 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7806 (mtm180) REVERT: D 17 TYR cc_start: 0.8800 (m-80) cc_final: 0.8542 (m-80) REVERT: D 134 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8803 (mt-10) REVERT: D 161 TYR cc_start: 0.9157 (m-80) cc_final: 0.8879 (m-80) REVERT: D 213 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7482 (mtm110) REVERT: D 271 GLU cc_start: 0.8524 (mp0) cc_final: 0.8272 (mp0) REVERT: E 134 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8900 (mt-10) REVERT: E 213 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7741 (mtp-110) REVERT: E 319 ARG cc_start: 0.8426 (mmt180) cc_final: 0.8218 (mmt180) REVERT: H 213 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7810 (mtm180) REVERT: I 17 TYR cc_start: 0.8807 (m-80) cc_final: 0.8549 (m-80) REVERT: I 134 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8814 (mt-10) REVERT: I 161 TYR cc_start: 0.9148 (m-80) cc_final: 0.8873 (m-80) REVERT: I 213 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7482 (mtm110) REVERT: I 271 GLU cc_start: 0.8506 (mp0) cc_final: 0.8256 (mp0) REVERT: J 134 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8902 (mt-10) REVERT: J 213 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7728 (mtp-110) outliers start: 67 outliers final: 40 residues processed: 313 average time/residue: 0.1649 time to fit residues: 81.7331 Evaluate side-chains 288 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 18 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 267 optimal weight: 0.0770 chunk 89 optimal weight: 0.7980 chunk 317 optimal weight: 8.9990 chunk 355 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 294 optimal weight: 0.4980 chunk 330 optimal weight: 6.9990 overall best weight: 1.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3738 r_free = 0.3738 target = 0.138932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106767 restraints weight = 35166.259| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.31 r_work: 0.3183 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1291 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= 0.140 Angle : 0.498 6.088 39040 Z= 0.259 Chirality : 0.042 0.152 4050 Planarity : 0.004 0.054 5170 Dihedral : 3.847 18.763 4030 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.00 % Allowed : 13.10 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.15), residues: 3640 helix: 1.70 (0.16), residues: 1070 sheet: -0.43 (0.19), residues: 820 loop : 0.45 (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 0.008 0.001 PHE J 204 TRP 0.003 0.001 TRP B 247 HIS 0.002 0.001 HIS I 217 Details of bonding type rmsd covalent geometry : bond 0.00329 (28760) covalent geometry : angle 0.49816 (39040) hydrogen bonds : bond 0.03783 ( 1220) hydrogen bonds : angle 5.08264 ( 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 367 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 284 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 ILE cc_start: 0.9026 (mm) cc_final: 0.8798 (mt) REVERT: C 127 GLN cc_start: 0.7764 (mt0) cc_final: 0.7563 (mt0) REVERT: C 213 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7756 (mtm180) REVERT: D 17 TYR cc_start: 0.8750 (m-80) cc_final: 0.8512 (m-80) REVERT: D 77 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8104 (mtt) REVERT: D 134 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8880 (mt-10) REVERT: D 161 TYR cc_start: 0.9095 (m-80) cc_final: 0.8838 (m-80) REVERT: D 213 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7384 (mtm110) REVERT: E 134 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8892 (mt-10) REVERT: E 213 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7734 (mtp-110) REVERT: E 319 ARG cc_start: 0.8445 (mmt180) cc_final: 0.8233 (mmt180) REVERT: H 13 ILE cc_start: 0.9034 (mm) cc_final: 0.8805 (mt) REVERT: H 213 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7750 (mtm180) REVERT: I 17 TYR cc_start: 0.8768 (m-80) cc_final: 0.8523 (m-80) REVERT: I 77 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8091 (mtt) REVERT: I 134 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8887 (mt-10) REVERT: I 161 TYR cc_start: 0.9091 (m-80) cc_final: 0.8838 (m-80) REVERT: I 213 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7381 (mtm110) REVERT: J 134 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8889 (mt-10) REVERT: J 213 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7731 (mtp-110) REVERT: J 319 ARG cc_start: 0.8435 (mmt180) cc_final: 0.8220 (mmt180) outliers start: 83 outliers final: 46 residues processed: 342 average time/residue: 0.1574 time to fit residues: 86.9670 Evaluate side-chains 298 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 C residue 165 VAL 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 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 165 VAL 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 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 77 MET 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 165 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 309 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 219 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 349 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 127 GLN H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103741 restraints weight = 35672.864| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.32 r_work: 0.3144 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 28760 Z= 0.229 Angle : 0.545 6.883 39040 Z= 0.281 Chirality : 0.044 0.146 4050 Planarity : 0.004 0.055 5170 Dihedral : 4.013 20.726 4030 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.53 % Allowed : 14.04 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.15), residues: 3640 helix: 1.58 (0.16), residues: 1070 sheet: -0.66 (0.19), residues: 860 loop : 0.40 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 227 TYR 0.009 0.001 TYR I 137 PHE 0.010 0.002 PHE C 68 TRP 0.004 0.001 TRP J 149 HIS 0.003 0.001 HIS I 217 Details of bonding type rmsd covalent geometry : bond 0.00551 (28760) covalent geometry : angle 0.54489 (39040) hydrogen bonds : bond 0.04184 ( 1220) hydrogen bonds : angle 5.12199 ( 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 326 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.709 Fit side-chains REVERT: B 267 LEU cc_start: 0.8357 (mt) cc_final: 0.8120 (mt) REVERT: C 261 MET cc_start: 0.8706 (mtm) cc_final: 0.8453 (mtp) REVERT: D 77 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8079 (mtt) REVERT: D 134 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8856 (mt-10) REVERT: D 213 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7513 (mtm110) REVERT: E 134 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8884 (mt-10) REVERT: E 213 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7759 (mtp-110) REVERT: E 319 ARG cc_start: 0.8507 (mmt180) cc_final: 0.8294 (mmt180) REVERT: G 267 LEU cc_start: 0.8349 (mt) cc_final: 0.8109 (mt) REVERT: H 213 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7786 (mtm180) REVERT: H 261 MET cc_start: 0.8418 (mtm) cc_final: 0.8005 (mtm) REVERT: I 77 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8078 (mtt) REVERT: I 134 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8879 (mt-10) REVERT: I 213 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7498 (mtm110) REVERT: J 134 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8899 (mt-10) REVERT: J 213 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7750 (mtp-110) REVERT: J 319 ARG cc_start: 0.8511 (mmt180) cc_final: 0.8294 (mmt180) outliers start: 70 outliers final: 45 residues processed: 304 average time/residue: 0.1690 time to fit residues: 82.3893 Evaluate side-chains 295 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 244 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 8.9990 chunk 170 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 120 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 146 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 353 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 overall best weight: 1.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3726 r_free = 0.3726 target = 0.138103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106426 restraints weight = 35324.875| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.31 r_work: 0.3176 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28760 Z= 0.146 Angle : 0.506 6.885 39040 Z= 0.260 Chirality : 0.042 0.146 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.845 19.038 4030 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.45 % Allowed : 14.55 % 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 aren not related in a simple way. whole: 0.74 (0.15), residues: 3640 helix: 1.69 (0.16), residues: 1070 sheet: -0.56 (0.19), residues: 820 loop : 0.44 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 41 TYR 0.007 0.001 TYR J 137 PHE 0.009 0.001 PHE B 223 TRP 0.003 0.001 TRP D 32 HIS 0.002 0.001 HIS G 253 Details of bonding type rmsd covalent geometry : bond 0.00347 (28760) covalent geometry : angle 0.50566 (39040) hydrogen bonds : bond 0.03717 ( 1220) hydrogen bonds : angle 4.97286 ( 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 339 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 271 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8502 (mp) REVERT: C 13 ILE cc_start: 0.9054 (mm) cc_final: 0.8839 (mt) REVERT: D 17 TYR cc_start: 0.8772 (m-80) cc_final: 0.8467 (m-80) REVERT: D 77 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8090 (mtt) REVERT: D 134 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8844 (mt-10) REVERT: D 161 TYR cc_start: 0.9133 (m-80) cc_final: 0.8813 (m-80) REVERT: D 213 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7505 (mtm110) REVERT: E 134 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8899 (mt-10) REVERT: E 213 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7790 (mtp-110) REVERT: E 319 ARG cc_start: 0.8467 (mmt180) cc_final: 0.8253 (mmt180) REVERT: F 175 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8515 (mp) REVERT: H 13 ILE cc_start: 0.9069 (mm) cc_final: 0.8851 (mt) REVERT: H 261 MET cc_start: 0.8440 (mtm) cc_final: 0.8088 (mtm) REVERT: I 17 TYR cc_start: 0.8782 (m-80) cc_final: 0.8472 (m-80) REVERT: I 77 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8079 (mtt) REVERT: I 134 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8856 (mt-10) REVERT: I 161 TYR cc_start: 0.9121 (m-80) cc_final: 0.8803 (m-80) REVERT: I 213 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7506 (mtm110) REVERT: J 134 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8906 (mt-10) REVERT: J 213 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7795 (mtp-110) REVERT: J 319 ARG cc_start: 0.8468 (mmt180) cc_final: 0.8251 (mmt180) outliers start: 68 outliers final: 51 residues processed: 319 average time/residue: 0.1558 time to fit residues: 79.6538 Evaluate side-chains 306 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 271 GLU 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 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 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 134 GLU Chi-restraints excluded: chain H residue 271 GLU 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 270 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 138 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 320 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 244 optimal weight: 0.1980 chunk 186 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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** I 194 ASN J 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106171 restraints weight = 35449.331| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.34 r_work: 0.3150 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28760 Z= 0.197 Angle : 0.533 7.178 39040 Z= 0.273 Chirality : 0.043 0.142 4050 Planarity : 0.004 0.054 5170 Dihedral : 3.941 20.074 4030 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.64 % Allowed : 15.09 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.15), residues: 3640 helix: 1.61 (0.16), residues: 1070 sheet: -0.65 (0.19), residues: 820 loop : 0.40 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 324 TYR 0.008 0.001 TYR D 137 PHE 0.010 0.002 PHE G 223 TRP 0.004 0.001 TRP D 149 HIS 0.002 0.001 HIS J 217 Details of bonding type rmsd covalent geometry : bond 0.00473 (28760) covalent geometry : angle 0.53303 (39040) hydrogen bonds : bond 0.03956 ( 1220) hydrogen bonds : angle 4.98833 ( 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 334 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 261 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8508 (mp) REVERT: C 349 TYR cc_start: 0.8803 (m-80) cc_final: 0.8594 (m-80) REVERT: D 77 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8111 (mtt) REVERT: D 134 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8848 (mt-10) REVERT: D 161 TYR cc_start: 0.9162 (m-80) cc_final: 0.8844 (m-80) REVERT: D 213 ARG cc_start: 0.8152 (mtp85) cc_final: 0.7568 (mtm110) REVERT: E 134 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8924 (mt-10) REVERT: E 213 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7806 (mtp-110) REVERT: E 319 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8289 (mmt180) REVERT: F 175 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8518 (mp) REVERT: H 261 MET cc_start: 0.8502 (mtm) cc_final: 0.8161 (mtm) REVERT: H 349 TYR cc_start: 0.8807 (m-80) cc_final: 0.8594 (m-80) REVERT: I 77 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: I 134 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8855 (mt-10) REVERT: I 161 TYR cc_start: 0.9151 (m-80) cc_final: 0.8830 (m-80) REVERT: I 213 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7525 (mtm110) REVERT: J 134 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8926 (mt-10) REVERT: J 213 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7798 (mtp-110) REVERT: J 319 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8293 (mmt180) outliers start: 73 outliers final: 56 residues processed: 312 average time/residue: 0.1639 time to fit residues: 82.0846 Evaluate side-chains 310 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 271 GLU 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 197 VAL 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 123 MET Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 142 THR 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 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 134 GLU Chi-restraints excluded: chain H residue 271 GLU 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 270 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 123 MET 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: 3.9990 chunk 248 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 203 optimal weight: 0.4980 chunk 209 optimal weight: 0.0060 chunk 50 optimal weight: 0.6980 chunk 221 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108740 restraints weight = 35372.364| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.32 r_work: 0.3199 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28760 Z= 0.116 Angle : 0.495 7.629 39040 Z= 0.253 Chirality : 0.041 0.145 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.733 17.812 4030 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.49 % Allowed : 15.52 % 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 aren not related in a simple way. whole: 0.82 (0.15), residues: 3640 helix: 1.77 (0.16), residues: 1070 sheet: -0.62 (0.19), residues: 820 loop : 0.53 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 262 TYR 0.008 0.001 TYR G 349 PHE 0.009 0.001 PHE A 337 TRP 0.005 0.001 TRP I 149 HIS 0.002 0.001 HIS J 253 Details of bonding type rmsd covalent geometry : bond 0.00271 (28760) covalent geometry : angle 0.49516 (39040) hydrogen bonds : bond 0.03470 ( 1220) hydrogen bonds : angle 4.84709 ( 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: 69 poor density : 283 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8489 (mp) REVERT: A 271 GLU cc_start: 0.8567 (mp0) cc_final: 0.8205 (mp0) REVERT: B 231 ASP cc_start: 0.8880 (m-30) cc_final: 0.8655 (m-30) REVERT: D 17 TYR cc_start: 0.8749 (m-80) cc_final: 0.8390 (m-80) REVERT: D 77 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8121 (mtt) REVERT: D 134 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8765 (mt-10) REVERT: D 161 TYR cc_start: 0.9077 (m-80) cc_final: 0.8765 (m-80) REVERT: D 213 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7454 (mtm110) REVERT: E 17 TYR cc_start: 0.8816 (m-80) cc_final: 0.8535 (m-80) REVERT: E 213 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7720 (mtp-110) REVERT: E 231 ASP cc_start: 0.8883 (m-30) cc_final: 0.8426 (m-30) REVERT: E 319 ARG cc_start: 0.8477 (mmt180) cc_final: 0.8254 (mmt180) REVERT: F 175 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8488 (mp) REVERT: G 231 ASP cc_start: 0.8870 (m-30) cc_final: 0.8646 (m-30) REVERT: H 13 ILE cc_start: 0.9025 (mm) cc_final: 0.8822 (mt) REVERT: H 261 MET cc_start: 0.8500 (mtm) cc_final: 0.8153 (mtm) REVERT: I 17 TYR cc_start: 0.8751 (m-80) cc_final: 0.8392 (m-80) REVERT: I 77 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8093 (mtt) REVERT: I 134 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8769 (mt-10) REVERT: I 161 TYR cc_start: 0.9066 (m-80) cc_final: 0.8754 (m-80) REVERT: I 213 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7462 (mtm110) REVERT: J 17 TYR cc_start: 0.8790 (m-80) cc_final: 0.8521 (m-80) REVERT: J 213 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7709 (mtp-110) REVERT: J 231 ASP cc_start: 0.8881 (m-30) cc_final: 0.8431 (m-30) REVERT: J 319 ARG cc_start: 0.8474 (mmt180) cc_final: 0.8251 (mmt180) outliers start: 69 outliers final: 52 residues processed: 333 average time/residue: 0.1667 time to fit residues: 89.4713 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 : 1.009 ------------------------------------------------------------------------------- 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 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL 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 271 GLU 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 270 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 123 MET 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 197 VAL 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 165 VAL Chi-restraints excluded: chain H residue 271 GLU 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 270 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 123 MET 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: 10.0000 chunk 11 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 chunk 216 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3730 r_free = 0.3730 target = 0.138263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106324 restraints weight = 35460.193| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.32 r_work: 0.3173 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28760 Z= 0.168 Angle : 0.524 8.478 39040 Z= 0.267 Chirality : 0.042 0.140 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.821 18.840 4030 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.20 % Allowed : 15.74 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 3640 helix: 1.72 (0.16), residues: 1070 sheet: -0.66 (0.19), residues: 820 loop : 0.49 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 41 TYR 0.008 0.001 TYR C 137 PHE 0.009 0.001 PHE H 337 TRP 0.003 0.001 TRP D 32 HIS 0.002 0.001 HIS J 217 Details of bonding type rmsd covalent geometry : bond 0.00403 (28760) covalent geometry : angle 0.52417 (39040) hydrogen bonds : bond 0.03750 ( 1220) hydrogen bonds : angle 4.87139 ( 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 317 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9195 (mtp) cc_final: 0.8980 (mtt) REVERT: C 261 MET cc_start: 0.8536 (mtm) cc_final: 0.8108 (ttm) REVERT: C 349 TYR cc_start: 0.8782 (m-80) cc_final: 0.8557 (m-80) REVERT: D 77 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8103 (mtt) REVERT: D 134 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8816 (mt-10) REVERT: D 161 TYR cc_start: 0.9136 (m-80) cc_final: 0.8821 (m-80) REVERT: D 213 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7524 (mtm110) REVERT: E 213 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7770 (mtp-110) REVERT: E 214 MET cc_start: 0.8645 (tpp) cc_final: 0.8440 (tpt) REVERT: E 319 ARG cc_start: 0.8479 (mmt180) cc_final: 0.8241 (mmt180) REVERT: F 140 MET cc_start: 0.9209 (mtp) cc_final: 0.8996 (mtt) REVERT: F 175 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8516 (mp) REVERT: H 140 MET cc_start: 0.9053 (mtm) cc_final: 0.8842 (mtm) REVERT: H 349 TYR cc_start: 0.8785 (m-80) cc_final: 0.8556 (m-80) REVERT: I 77 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8072 (mtt) REVERT: I 134 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (mt-10) REVERT: I 161 TYR cc_start: 0.9132 (m-80) cc_final: 0.8822 (m-80) REVERT: I 213 ARG cc_start: 0.8130 (mtp85) cc_final: 0.7517 (mtm110) REVERT: J 213 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7782 (mtp-110) REVERT: J 214 MET cc_start: 0.8651 (tpp) cc_final: 0.8444 (tpt) REVERT: J 319 ARG cc_start: 0.8486 (mmt180) cc_final: 0.8249 (mmt180) outliers start: 61 outliers final: 51 residues processed: 300 average time/residue: 0.1721 time to fit residues: 82.5965 Evaluate side-chains 306 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 250 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 197 VAL 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 271 GLU 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 270 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 123 MET 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 197 VAL 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 271 GLU 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 270 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 123 MET 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: 9.9990 chunk 201 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 308 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 = 0.140480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109035 restraints weight = 35153.738| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.30 r_work: 0.3202 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28760 Z= 0.121 Angle : 0.501 7.755 39040 Z= 0.255 Chirality : 0.041 0.143 4050 Planarity : 0.004 0.058 5170 Dihedral : 3.700 17.576 4030 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.06 % Allowed : 16.03 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.15), residues: 3640 helix: 1.79 (0.16), residues: 1070 sheet: -0.63 (0.19), residues: 820 loop : 0.55 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 262 TYR 0.007 0.001 TYR D 349 PHE 0.009 0.001 PHE A 337 TRP 0.003 0.001 TRP I 149 HIS 0.002 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00286 (28760) covalent geometry : angle 0.50092 (39040) hydrogen bonds : bond 0.03480 ( 1220) hydrogen bonds : angle 4.78379 ( 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 333 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 276 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9181 (mtp) cc_final: 0.8952 (mtt) REVERT: C 13 ILE cc_start: 0.9006 (mm) cc_final: 0.8774 (mt) REVERT: C 47 LEU cc_start: 0.8336 (tp) cc_final: 0.7979 (tp) REVERT: D 77 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8072 (mtt) REVERT: D 134 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8768 (mt-10) REVERT: D 161 TYR cc_start: 0.9071 (m-80) cc_final: 0.8762 (m-80) REVERT: D 213 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7449 (mtm110) REVERT: E 17 TYR cc_start: 0.8821 (m-80) cc_final: 0.8555 (m-80) REVERT: E 213 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7731 (mtp-110) REVERT: E 231 ASP cc_start: 0.8914 (m-30) cc_final: 0.8453 (m-30) REVERT: E 319 ARG cc_start: 0.8471 (mmt180) cc_final: 0.8243 (mmt180) REVERT: F 140 MET cc_start: 0.9192 (mtp) cc_final: 0.8964 (mtt) REVERT: F 175 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8507 (mp) REVERT: G 231 ASP cc_start: 0.8871 (m-30) cc_final: 0.8635 (m-30) REVERT: H 13 ILE cc_start: 0.9018 (mm) cc_final: 0.8817 (mt) REVERT: H 47 LEU cc_start: 0.8333 (tp) cc_final: 0.7976 (tp) REVERT: H 140 MET cc_start: 0.8996 (mtm) cc_final: 0.8722 (mtm) REVERT: I 77 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8042 (mtt) REVERT: I 134 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8780 (mt-10) REVERT: I 161 TYR cc_start: 0.9064 (m-80) cc_final: 0.8755 (m-80) REVERT: I 213 ARG cc_start: 0.8054 (mtp85) cc_final: 0.7454 (mtm110) REVERT: J 17 TYR cc_start: 0.8816 (m-80) cc_final: 0.8539 (m-80) REVERT: J 213 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7737 (mtp-110) REVERT: J 231 ASP cc_start: 0.8914 (m-30) cc_final: 0.8466 (m-30) REVERT: J 319 ARG cc_start: 0.8466 (mmt180) cc_final: 0.8238 (mmt180) outliers start: 57 outliers final: 49 residues processed: 321 average time/residue: 0.1629 time to fit residues: 84.0055 Evaluate side-chains 313 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 197 VAL 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 271 GLU 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 270 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 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 VAL 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 271 GLU 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 270 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: 5.9990 chunk 285 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 321 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 241 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3756 r_free = 0.3756 target = 0.140435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108712 restraints weight = 35206.838| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.32 r_work: 0.3203 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28760 Z= 0.122 Angle : 0.498 7.610 39040 Z= 0.254 Chirality : 0.041 0.143 4050 Planarity : 0.004 0.057 5170 Dihedral : 3.665 17.025 4030 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.09 % Allowed : 15.88 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.15), residues: 3640 helix: 1.80 (0.16), residues: 1070 sheet: -0.61 (0.19), residues: 820 loop : 0.56 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 227 TYR 0.009 0.001 TYR G 349 PHE 0.012 0.001 PHE D 223 TRP 0.003 0.001 TRP H 202 HIS 0.002 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00287 (28760) covalent geometry : angle 0.49757 (39040) hydrogen bonds : bond 0.03481 ( 1220) hydrogen bonds : angle 4.75474 ( 3270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5561.37 seconds wall clock time: 96 minutes 23.73 seconds (5783.73 seconds total)