Starting phenix.real_space_refine on Mon Jun 23 22:12:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c28_45137/06_2025/9c28_45137.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c28_45137/06_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_45137/06_2025/9c28_45137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c28_45137/06_2025/9c28_45137.map" model { file = "/net/cci-nas-00/data/ceres_data/9c28_45137/06_2025/9c28_45137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c28_45137/06_2025/9c28_45137.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 3} 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: C, B, E, D, G, F, I, H, J Time building chain proxies: 8.45, per 1000 atoms: 0.30 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: 6.91 Conformation dependent library (CDL) restraints added in 3.7 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6680 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 37.0% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.46 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: 10.21 Time building geometry restraints manager: 8.11 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: 0.24 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 1.100 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: 1.060 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 54.150 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.004 0.001 TRP I 202 HIS 0.002 0.000 HIS G 217 PHE 0.007 0.001 PHE B 204 TYR 0.004 0.001 TYR C 137 ARG 0.003 0.000 ARG G 262 Details of bonding type rmsd hydrogen bonds : bond 0.18638 ( 1220) hydrogen bonds : angle 6.50578 ( 3270) covalent geometry : bond 0.00231 (28760) covalent geometry : angle 0.48163 (39040) *********************** 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 : 3.402 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: 0.4371 time to fit residues: 219.7489 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 : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 282 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 326 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103858 restraints weight = 35697.186| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.33 r_work: 0.3142 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 28760 Z= 0.253 Angle : 0.572 5.165 39040 Z= 0.302 Chirality : 0.045 0.142 4050 Planarity : 0.004 0.056 5170 Dihedral : 4.001 19.287 4030 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.60 % Allowed : 13.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3640 helix: 1.67 (0.16), residues: 1070 sheet: -0.51 (0.18), residues: 850 loop : 0.47 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 130 HIS 0.004 0.001 HIS A 8 PHE 0.012 0.002 PHE H 98 TYR 0.010 0.001 TYR D 137 ARG 0.003 0.000 ARG J 41 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 1220) hydrogen bonds : angle 5.44406 ( 3270) covalent geometry : bond 0.00606 (28760) covalent geometry : angle 0.57177 (39040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 274 time to evaluate : 8.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7521 (mtm180) REVERT: C 213 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7900 (mtm180) REVERT: C 289 ASP cc_start: 0.7028 (p0) cc_final: 0.6694 (p0) REVERT: D 134 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8729 (mt-10) REVERT: D 161 TYR cc_start: 0.9152 (m-80) cc_final: 0.8858 (m-80) REVERT: D 213 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7579 (mtm110) REVERT: E 213 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7864 (mtp-110) REVERT: G 213 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7513 (mtm180) REVERT: H 213 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7895 (mtm180) REVERT: H 289 ASP cc_start: 0.7039 (p0) cc_final: 0.6705 (p0) REVERT: I 134 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8723 (mt-10) REVERT: I 161 TYR cc_start: 0.9146 (m-80) cc_final: 0.8856 (m-80) REVERT: I 213 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7583 (mtm110) REVERT: J 213 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7860 (mtp-110) outliers start: 72 outliers final: 32 residues processed: 310 average time/residue: 0.6599 time to fit residues: 326.4131 Evaluate side-chains 292 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 6.011 ------------------------------------------------------------------------------- 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 176 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 226 optimal weight: 0.2980 chunk 133 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 356 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 359 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.136731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104440 restraints weight = 35473.101| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.33 r_work: 0.3149 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 28760 Z= 0.212 Angle : 0.533 6.143 39040 Z= 0.278 Chirality : 0.043 0.144 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.981 20.247 4030 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.24 % Allowed : 13.94 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3640 helix: 1.66 (0.16), residues: 1070 sheet: -0.51 (0.19), residues: 860 loop : 0.45 (0.17), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 149 HIS 0.003 0.001 HIS D 217 PHE 0.009 0.002 PHE C 68 TYR 0.008 0.001 TYR D 137 ARG 0.002 0.000 ARG I 324 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 1220) hydrogen bonds : angle 5.22837 ( 3270) covalent geometry : bond 0.00508 (28760) covalent geometry : angle 0.53270 (39040) *********************** 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 324 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 213 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7866 (mtm180) REVERT: D 17 TYR cc_start: 0.8814 (m-80) cc_final: 0.8560 (m-80) REVERT: D 134 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8822 (mt-10) REVERT: D 161 TYR cc_start: 0.9144 (m-80) cc_final: 0.8866 (m-80) REVERT: D 213 ARG cc_start: 0.8183 (mtp85) cc_final: 0.7584 (mtm110) REVERT: D 267 LEU cc_start: 0.8211 (mt) cc_final: 0.7263 (mt) REVERT: E 134 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8916 (mt-10) REVERT: E 213 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7815 (mtp-110) REVERT: F 267 LEU cc_start: 0.8090 (mt) cc_final: 0.7065 (mt) REVERT: H 213 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7875 (mtm180) REVERT: I 17 TYR cc_start: 0.8811 (m-80) cc_final: 0.8552 (m-80) REVERT: I 134 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8828 (mt-10) REVERT: I 161 TYR cc_start: 0.9140 (m-80) cc_final: 0.8862 (m-80) REVERT: I 213 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7559 (mtm110) REVERT: I 267 LEU cc_start: 0.8212 (mt) cc_final: 0.7261 (mt) REVERT: J 134 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8910 (mt-10) REVERT: J 213 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7815 (mtp-110) outliers start: 62 outliers final: 41 residues processed: 304 average time/residue: 0.4344 time to fit residues: 208.6208 Evaluate side-chains 288 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 3.439 ------------------------------------------------------------------------------- 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 A residue 328 ILE Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 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 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 108 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 273 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.140691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108216 restraints weight = 35256.715| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.35 r_work: 0.3198 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 28760 Z= 0.116 Angle : 0.488 6.460 39040 Z= 0.255 Chirality : 0.041 0.159 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.728 17.460 4030 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.18 % Allowed : 12.82 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3640 helix: 1.72 (0.16), residues: 1070 sheet: -0.40 (0.19), residues: 820 loop : 0.53 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 247 HIS 0.002 0.001 HIS C 217 PHE 0.008 0.001 PHE E 204 TYR 0.005 0.001 TYR J 137 ARG 0.002 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 1220) hydrogen bonds : angle 5.04204 ( 3270) covalent geometry : bond 0.00264 (28760) covalent geometry : angle 0.48809 (39040) *********************** 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 366 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 278 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLU cc_start: 0.8326 (mp0) cc_final: 0.8094 (mp0) REVERT: B 231 ASP cc_start: 0.8873 (m-30) cc_final: 0.8659 (m-30) REVERT: C 13 ILE cc_start: 0.9022 (mm) cc_final: 0.8800 (mt) REVERT: C 289 ASP cc_start: 0.6931 (p0) cc_final: 0.6569 (p0) REVERT: D 17 TYR cc_start: 0.8759 (m-80) cc_final: 0.8507 (m-80) REVERT: D 77 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8132 (mtt) REVERT: D 134 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8901 (mt-10) REVERT: D 161 TYR cc_start: 0.9057 (m-80) cc_final: 0.8806 (m-80) REVERT: D 213 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7360 (mtm110) REVERT: E 134 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8891 (mt-10) REVERT: E 213 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7740 (mtp-110) REVERT: E 231 ASP cc_start: 0.8895 (m-30) cc_final: 0.8470 (m-30) REVERT: G 231 ASP cc_start: 0.8866 (m-30) cc_final: 0.8658 (m-30) REVERT: H 13 ILE cc_start: 0.9023 (mm) cc_final: 0.8799 (mt) REVERT: I 17 TYR cc_start: 0.8763 (m-80) cc_final: 0.8508 (m-80) REVERT: I 77 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8132 (mtt) REVERT: I 134 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8902 (mt-10) REVERT: I 161 TYR cc_start: 0.9056 (m-80) cc_final: 0.8798 (m-80) REVERT: I 213 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7364 (mtm110) REVERT: J 134 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8889 (mt-10) REVERT: J 213 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7747 (mtp-110) outliers start: 88 outliers final: 46 residues processed: 344 average time/residue: 0.3950 time to fit residues: 222.6202 Evaluate side-chains 292 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 3.230 ------------------------------------------------------------------------------- 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 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 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 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 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 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 H residue 165 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 70 optimal weight: 0.8980 chunk 277 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 94 optimal weight: 0.2980 chunk 324 optimal weight: 0.9990 chunk 297 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 174 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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** D 194 ASN E 152 ASN F 152 ASN F 194 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.143173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110699 restraints weight = 34987.485| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.40 r_work: 0.3227 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 28760 Z= 0.097 Angle : 0.471 5.571 39040 Z= 0.244 Chirality : 0.040 0.172 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.585 15.745 4030 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.60 % Allowed : 13.25 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 3640 helix: 1.84 (0.16), residues: 1070 sheet: -0.35 (0.19), residues: 800 loop : 0.60 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 32 HIS 0.002 0.000 HIS H 253 PHE 0.012 0.001 PHE A 223 TYR 0.008 0.001 TYR B 349 ARG 0.002 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 1220) hydrogen bonds : angle 4.82415 ( 3270) covalent geometry : bond 0.00219 (28760) covalent geometry : angle 0.47092 (39040) *********************** 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 370 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 3.383 Fit side-chains revert: symmetry clash REVERT: A 267 LEU cc_start: 0.7868 (mt) cc_final: 0.7379 (mt) REVERT: A 271 GLU cc_start: 0.8408 (mp0) cc_final: 0.8206 (mp0) REVERT: B 267 LEU cc_start: 0.8235 (mt) cc_final: 0.7956 (mt) REVERT: C 13 ILE cc_start: 0.8906 (mm) cc_final: 0.8698 (mt) REVERT: C 47 LEU cc_start: 0.8152 (tp) cc_final: 0.7821 (tp) REVERT: D 17 TYR cc_start: 0.8614 (m-80) cc_final: 0.8319 (m-80) REVERT: D 77 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7939 (mtt) REVERT: D 134 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8587 (mt-10) REVERT: D 161 TYR cc_start: 0.8888 (m-80) cc_final: 0.8580 (m-80) REVERT: D 213 ARG cc_start: 0.7701 (mtp85) cc_final: 0.7093 (mtm110) REVERT: D 271 GLU cc_start: 0.8395 (mp0) cc_final: 0.8037 (mp0) REVERT: E 134 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8620 (mt-10) REVERT: E 140 MET cc_start: 0.8256 (mtm) cc_final: 0.8054 (mtt) REVERT: E 213 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7393 (mtp-110) REVERT: E 231 ASP cc_start: 0.8731 (m-30) cc_final: 0.8244 (m-30) REVERT: G 267 LEU cc_start: 0.8230 (mt) cc_final: 0.7949 (mt) REVERT: H 13 ILE cc_start: 0.8891 (mm) cc_final: 0.8680 (mt) REVERT: H 47 LEU cc_start: 0.8144 (tp) cc_final: 0.7811 (tp) REVERT: I 17 TYR cc_start: 0.8617 (m-80) cc_final: 0.8322 (m-80) REVERT: I 77 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7933 (mtt) REVERT: I 134 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8584 (mt-10) REVERT: I 161 TYR cc_start: 0.8894 (m-80) cc_final: 0.8587 (m-80) REVERT: I 213 ARG cc_start: 0.7698 (mtp85) cc_final: 0.7087 (mtm110) REVERT: I 271 GLU cc_start: 0.8403 (mp0) cc_final: 0.8046 (mp0) REVERT: J 134 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8615 (mt-10) REVERT: J 213 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7394 (mtp-110) REVERT: J 231 ASP cc_start: 0.8676 (m-30) cc_final: 0.8200 (m-30) outliers start: 72 outliers final: 51 residues processed: 345 average time/residue: 0.3763 time to fit residues: 212.5530 Evaluate side-chains 324 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 328 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 165 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 328 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 294 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 chunk 210 optimal weight: 0.0980 chunk 283 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN J 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103231 restraints weight = 35848.451| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.35 r_work: 0.3131 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 28760 Z= 0.261 Angle : 0.567 7.100 39040 Z= 0.292 Chirality : 0.044 0.165 4050 Planarity : 0.004 0.053 5170 Dihedral : 4.008 20.220 4030 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 14.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.15), residues: 3640 helix: 1.57 (0.16), residues: 1070 sheet: -0.54 (0.19), residues: 810 loop : 0.37 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 219 HIS 0.004 0.001 HIS E 217 PHE 0.013 0.002 PHE A 223 TYR 0.010 0.001 TYR E 17 ARG 0.002 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04256 ( 1220) hydrogen bonds : angle 5.03449 ( 3270) covalent geometry : bond 0.00627 (28760) covalent geometry : angle 0.56728 (39040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 273 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 MET cc_start: 0.9213 (mtp) cc_final: 0.8802 (mtt) REVERT: B 213 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7447 (mtm180) REVERT: D 77 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8126 (mtt) REVERT: D 134 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8830 (mt-10) REVERT: D 161 TYR cc_start: 0.9169 (m-80) cc_final: 0.8898 (m-80) REVERT: D 213 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7575 (mtm110) REVERT: E 134 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8931 (mt-10) REVERT: E 213 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7901 (mtp-110) REVERT: G 140 MET cc_start: 0.9225 (mtp) cc_final: 0.8815 (mtt) REVERT: G 213 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7389 (mtm110) REVERT: I 77 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8131 (mtt) REVERT: I 134 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8839 (mt-10) REVERT: I 161 TYR cc_start: 0.9163 (m-80) cc_final: 0.8891 (m-80) REVERT: I 213 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7563 (mtm110) REVERT: J 134 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8939 (mt-10) REVERT: J 213 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7777 (mtp-110) outliers start: 67 outliers final: 45 residues processed: 313 average time/residue: 0.4083 time to fit residues: 202.8204 Evaluate side-chains 307 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 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 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 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 119 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 352 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108647 restraints weight = 35007.131| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.33 r_work: 0.3204 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28760 Z= 0.113 Angle : 0.488 6.847 39040 Z= 0.251 Chirality : 0.041 0.166 4050 Planarity : 0.004 0.054 5170 Dihedral : 3.745 17.435 4030 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.09 % Allowed : 15.27 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.15), residues: 3640 helix: 1.72 (0.16), residues: 1070 sheet: -0.56 (0.19), residues: 820 loop : 0.49 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 32 HIS 0.002 0.001 HIS E 217 PHE 0.011 0.001 PHE F 223 TYR 0.006 0.001 TYR C 349 ARG 0.002 0.000 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1220) hydrogen bonds : angle 4.84674 ( 3270) covalent geometry : bond 0.00262 (28760) covalent geometry : angle 0.48798 (39040) *********************** 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 355 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 297 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 LEU cc_start: 0.8337 (tp) cc_final: 0.7992 (tp) REVERT: C 309 ILE cc_start: 0.8803 (tt) cc_final: 0.8588 (pt) REVERT: D 17 TYR cc_start: 0.8779 (m-80) cc_final: 0.8481 (m-80) REVERT: D 77 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8115 (mtt) REVERT: D 134 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8745 (mt-10) REVERT: D 161 TYR cc_start: 0.9067 (m-80) cc_final: 0.8819 (m-80) REVERT: D 213 ARG cc_start: 0.8005 (mtp85) cc_final: 0.7404 (mtm110) REVERT: E 134 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8857 (mt-10) REVERT: E 213 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7755 (mtp-110) REVERT: E 231 ASP cc_start: 0.8920 (m-30) cc_final: 0.8486 (m-30) REVERT: H 47 LEU cc_start: 0.8332 (tp) cc_final: 0.7987 (tp) REVERT: H 309 ILE cc_start: 0.8795 (tt) cc_final: 0.8575 (pt) REVERT: I 17 TYR cc_start: 0.8792 (m-80) cc_final: 0.8416 (m-80) REVERT: I 77 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8131 (mtt) REVERT: I 134 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8745 (mt-10) REVERT: I 161 TYR cc_start: 0.9060 (m-80) cc_final: 0.8807 (m-80) REVERT: I 213 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7403 (mtm110) REVERT: J 17 TYR cc_start: 0.8844 (m-80) cc_final: 0.8538 (m-80) REVERT: J 134 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8943 (mt-10) REVERT: J 213 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7753 (mtp-110) REVERT: J 231 ASP cc_start: 0.8916 (m-30) cc_final: 0.8497 (m-30) outliers start: 58 outliers final: 47 residues processed: 335 average time/residue: 0.4115 time to fit residues: 222.0445 Evaluate side-chains 327 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 3.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 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 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 328 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 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 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 328 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 15 optimal weight: 4.9990 chunk 324 optimal weight: 0.3980 chunk 272 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.136582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104420 restraints weight = 35548.446| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.31 r_work: 0.3153 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28760 Z= 0.226 Angle : 0.549 7.717 39040 Z= 0.282 Chirality : 0.044 0.161 4050 Planarity : 0.004 0.054 5170 Dihedral : 3.963 19.839 4030 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.99 % Allowed : 16.14 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3640 helix: 1.58 (0.16), residues: 1070 sheet: -0.63 (0.19), residues: 810 loop : 0.36 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 149 HIS 0.004 0.001 HIS D 217 PHE 0.012 0.002 PHE D 223 TYR 0.008 0.001 TYR J 137 ARG 0.003 0.000 ARG J 324 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 1220) hydrogen bonds : angle 4.96610 ( 3270) covalent geometry : bond 0.00545 (28760) covalent geometry : angle 0.54936 (39040) *********************** 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 326 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 271 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9224 (mtp) cc_final: 0.9017 (mtt) REVERT: B 140 MET cc_start: 0.9233 (mtp) cc_final: 0.8812 (mtt) REVERT: B 213 ARG cc_start: 0.8072 (mtp85) cc_final: 0.7461 (mtm180) REVERT: D 77 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: D 134 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8840 (mt-10) REVERT: D 161 TYR cc_start: 0.9177 (m-80) cc_final: 0.8846 (m-80) REVERT: D 213 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7573 (mtm110) REVERT: E 134 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8966 (mt-10) REVERT: E 213 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7899 (mtp-110) REVERT: E 214 MET cc_start: 0.8946 (tpt) cc_final: 0.8075 (tpp) REVERT: F 140 MET cc_start: 0.9228 (mtp) cc_final: 0.9019 (mtt) REVERT: G 140 MET cc_start: 0.9231 (mtp) cc_final: 0.8801 (mtt) REVERT: G 213 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7439 (mtm180) REVERT: I 17 TYR cc_start: 0.8796 (m-80) cc_final: 0.8532 (m-80) REVERT: I 77 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8113 (mtt) REVERT: I 134 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8841 (mt-10) REVERT: I 161 TYR cc_start: 0.9172 (m-80) cc_final: 0.8838 (m-80) REVERT: I 213 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7574 (mtm110) REVERT: J 134 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8973 (mt-10) REVERT: J 213 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7870 (mtp-110) outliers start: 55 outliers final: 46 residues processed: 309 average time/residue: 0.4126 time to fit residues: 204.2129 Evaluate side-chains 303 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 271 GLU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 173 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 334 optimal weight: 7.9990 chunk 293 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 349 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109582 restraints weight = 34968.101| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.33 r_work: 0.3221 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28760 Z= 0.110 Angle : 0.496 7.477 39040 Z= 0.255 Chirality : 0.041 0.161 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.706 16.890 4030 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.95 % Allowed : 16.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3640 helix: 1.68 (0.16), residues: 1070 sheet: -0.49 (0.20), residues: 800 loop : 0.50 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 130 HIS 0.002 0.001 HIS J 253 PHE 0.009 0.001 PHE F 223 TYR 0.008 0.001 TYR G 349 ARG 0.002 0.000 ARG D 262 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 1220) hydrogen bonds : angle 4.85042 ( 3270) covalent geometry : bond 0.00255 (28760) covalent geometry : angle 0.49564 (39040) *********************** 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 347 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 293 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 LEU cc_start: 0.8320 (tp) cc_final: 0.7977 (tp) REVERT: C 349 TYR cc_start: 0.8769 (m-80) cc_final: 0.8494 (m-80) REVERT: D 17 TYR cc_start: 0.8737 (m-80) cc_final: 0.8357 (m-80) REVERT: D 77 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8062 (mtt) REVERT: D 134 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8789 (mt-10) REVERT: D 161 TYR cc_start: 0.9028 (m-80) cc_final: 0.8736 (m-80) REVERT: D 213 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7419 (mtm110) REVERT: E 17 TYR cc_start: 0.8817 (m-80) cc_final: 0.8501 (m-80) REVERT: E 134 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8892 (mt-10) REVERT: E 213 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7752 (mtp-110) REVERT: E 214 MET cc_start: 0.8752 (tpt) cc_final: 0.7949 (tpt) REVERT: E 231 ASP cc_start: 0.8900 (m-30) cc_final: 0.8447 (m-30) REVERT: H 47 LEU cc_start: 0.8310 (tp) cc_final: 0.7965 (tp) REVERT: H 349 TYR cc_start: 0.8762 (m-80) cc_final: 0.8487 (m-80) REVERT: I 17 TYR cc_start: 0.8749 (m-80) cc_final: 0.8442 (m-80) REVERT: I 77 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8043 (mtt) REVERT: I 134 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8787 (mt-10) REVERT: I 161 TYR cc_start: 0.9024 (m-80) cc_final: 0.8722 (m-80) REVERT: I 213 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7417 (mtm110) REVERT: J 17 TYR cc_start: 0.8825 (m-80) cc_final: 0.8551 (m-80) REVERT: J 213 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7744 (mtp-110) REVERT: J 231 ASP cc_start: 0.8866 (m-30) cc_final: 0.8418 (m-30) outliers start: 54 outliers final: 45 residues processed: 332 average time/residue: 0.4024 time to fit residues: 218.6423 Evaluate side-chains 324 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 274 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 165 VAL 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 E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 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 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 334 optimal weight: 3.9990 chunk 311 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 271 optimal weight: 0.0980 chunk 339 optimal weight: 0.7980 chunk 289 optimal weight: 0.8980 chunk 270 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108487 restraints weight = 35042.024| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.33 r_work: 0.3209 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28760 Z= 0.126 Angle : 0.510 7.933 39040 Z= 0.261 Chirality : 0.042 0.158 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.680 16.642 4030 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.99 % Allowed : 16.28 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3640 helix: 1.68 (0.16), residues: 1070 sheet: -0.49 (0.20), residues: 800 loop : 0.51 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 32 HIS 0.002 0.001 HIS B 217 PHE 0.009 0.001 PHE I 223 TYR 0.009 0.001 TYR G 349 ARG 0.002 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1220) hydrogen bonds : angle 4.83741 ( 3270) covalent geometry : bond 0.00295 (28760) covalent geometry : angle 0.50989 (39040) ********************** 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 337 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.9219 (mtp) cc_final: 0.8995 (mtt) REVERT: C 47 LEU cc_start: 0.8333 (tp) cc_final: 0.7991 (tp) REVERT: C 349 TYR cc_start: 0.8767 (m-80) cc_final: 0.8466 (m-80) REVERT: D 77 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8046 (mtt) REVERT: D 134 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8798 (mt-10) REVERT: D 161 TYR cc_start: 0.9081 (m-80) cc_final: 0.8768 (m-80) REVERT: D 213 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7437 (mtm110) REVERT: D 261 MET cc_start: 0.8237 (mtp) cc_final: 0.7926 (ttm) REVERT: E 17 TYR cc_start: 0.8838 (m-80) cc_final: 0.8580 (m-80) REVERT: E 134 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8900 (mt-10) REVERT: E 213 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7812 (mtp-110) REVERT: E 214 MET cc_start: 0.8807 (tpt) cc_final: 0.8057 (tpt) REVERT: E 231 ASP cc_start: 0.8892 (m-30) cc_final: 0.8450 (m-30) REVERT: F 140 MET cc_start: 0.9219 (mtp) cc_final: 0.8994 (mtt) REVERT: H 47 LEU cc_start: 0.8326 (tp) cc_final: 0.7985 (tp) REVERT: H 349 TYR cc_start: 0.8754 (m-80) cc_final: 0.8453 (m-80) REVERT: I 17 TYR cc_start: 0.8776 (m-80) cc_final: 0.8460 (m-80) REVERT: I 77 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8035 (mtt) REVERT: I 134 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8802 (mt-10) REVERT: I 161 TYR cc_start: 0.9038 (m-80) cc_final: 0.8738 (m-80) REVERT: I 213 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7430 (mtm110) REVERT: J 17 TYR cc_start: 0.8852 (m-80) cc_final: 0.8556 (m-80) REVERT: J 213 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7774 (mtp-110) REVERT: J 231 ASP cc_start: 0.8904 (m-30) cc_final: 0.8458 (m-30) outliers start: 55 outliers final: 48 residues processed: 323 average time/residue: 0.3993 time to fit residues: 210.0405 Evaluate side-chains 331 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 16 MET 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 165 VAL 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 E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 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 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 123 optimal weight: 0.2980 chunk 286 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 345 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104608 restraints weight = 35599.451| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.32 r_work: 0.3155 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 28760 Z= 0.212 Angle : 0.559 8.815 39040 Z= 0.287 Chirality : 0.044 0.164 4050 Planarity : 0.004 0.053 5170 Dihedral : 3.944 19.309 4030 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 16.64 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3640 helix: 1.54 (0.16), residues: 1070 sheet: -0.62 (0.19), residues: 820 loop : 0.41 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 219 HIS 0.004 0.001 HIS D 217 PHE 0.012 0.002 PHE I 256 TYR 0.009 0.001 TYR G 349 ARG 0.001 0.000 ARG F 213 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 1220) hydrogen bonds : angle 4.99437 ( 3270) covalent geometry : bond 0.00511 (28760) covalent geometry : angle 0.55894 (39040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14005.28 seconds wall clock time: 243 minutes 49.93 seconds (14629.93 seconds total)