Starting phenix.real_space_refine on Mon May 26 02:48:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c28_45137/05_2025/9c28_45137.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c28_45137/05_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_45137/05_2025/9c28_45137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c28_45137/05_2025/9c28_45137.map" model { file = "/net/cci-nas-00/data/ceres_data/9c28_45137/05_2025/9c28_45137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c28_45137/05_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-5687/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: 7.73, per 1000 atoms: 0.28 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: 6.29 Conformation dependent library (CDL) restraints added in 3.4 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: 3.90 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: 9.65 Time building geometry restraints manager: 7.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9360 1.35 - 1.46: 6890 1.46 - 1.58: 12150 1.58 - 1.70: 0 1.70 - 1.81: 360 Bond restraints: 28760 Sorted by residual: bond pdb=" CB MET C 121 " pdb=" CG MET C 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.53e-01 bond pdb=" CB MET E 121 " pdb=" CG MET E 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.43e-01 bond pdb=" CB MET A 121 " pdb=" CG MET A 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.43e-01 bond pdb=" CB MET F 121 " pdb=" CG MET F 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.43e-01 bond pdb=" CB MET H 121 " pdb=" CG MET H 121 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.41e-01 ... (remaining 28755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 38033 1.21 - 2.42: 666 2.42 - 3.63: 281 3.63 - 4.84: 50 4.84 - 6.05: 10 Bond angle restraints: 39040 Sorted by residual: angle pdb=" N ARG J 341 " pdb=" CA ARG J 341 " pdb=" C ARG J 341 " ideal model delta sigma weight residual 109.81 114.44 -4.63 2.21e+00 2.05e-01 4.40e+00 angle pdb=" N ARG B 341 " pdb=" CA ARG B 341 " pdb=" C ARG B 341 " ideal model delta sigma weight residual 109.81 114.42 -4.61 2.21e+00 2.05e-01 4.34e+00 angle pdb=" N ARG C 341 " pdb=" CA ARG C 341 " pdb=" C ARG C 341 " ideal model delta sigma weight residual 109.81 114.41 -4.60 2.21e+00 2.05e-01 4.33e+00 angle pdb=" N ARG H 341 " pdb=" CA ARG H 341 " pdb=" C ARG H 341 " ideal model delta sigma weight residual 109.81 114.41 -4.60 2.21e+00 2.05e-01 4.33e+00 angle pdb=" N ARG F 341 " pdb=" CA ARG F 341 " pdb=" C ARG F 341 " ideal model delta sigma weight residual 109.81 114.41 -4.60 2.21e+00 2.05e-01 4.32e+00 ... (remaining 39035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 15098 17.72 - 35.43: 1392 35.43 - 53.15: 350 53.15 - 70.86: 60 70.86 - 88.58: 40 Dihedral angle restraints: 16940 sinusoidal: 6450 harmonic: 10490 Sorted by residual: dihedral pdb=" CG ARG G 340 " pdb=" CD ARG G 340 " pdb=" NE ARG G 340 " pdb=" CZ ARG G 340 " ideal model delta sinusoidal sigma weight residual 180.00 -136.78 -43.22 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG B 340 " pdb=" CD ARG B 340 " pdb=" NE ARG B 340 " pdb=" CZ ARG B 340 " ideal model delta sinusoidal sigma weight residual -180.00 -136.78 -43.22 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG J 340 " pdb=" CD ARG J 340 " pdb=" NE ARG J 340 " pdb=" CZ ARG J 340 " ideal model delta sinusoidal sigma weight residual -180.00 -136.78 -43.22 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 16937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2261 0.027 - 0.053: 1149 0.053 - 0.080: 383 0.080 - 0.107: 197 0.107 - 0.133: 60 Chirality restraints: 4050 Sorted by residual: chirality pdb=" CA ILE H 325 " pdb=" N ILE H 325 " pdb=" C ILE H 325 " pdb=" CB ILE H 325 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE G 325 " pdb=" N ILE G 325 " pdb=" C ILE G 325 " pdb=" CB ILE G 325 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 325 " pdb=" N ILE A 325 " pdb=" C ILE A 325 " pdb=" CB ILE A 325 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 4047 not shown) Planarity restraints: 5170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY I 159 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO I 160 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 160 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 159 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO D 160 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 160 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 160 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY J 159 " -0.038 5.00e-02 4.00e+02 5.80e-02 5.39e+00 pdb=" N PRO J 160 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 160 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 160 " -0.032 5.00e-02 4.00e+02 ... (remaining 5167 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6602 2.78 - 3.31: 26093 3.31 - 3.84: 50179 3.84 - 4.37: 59444 4.37 - 4.90: 103636 Nonbonded interactions: 245954 Sorted by model distance: nonbonded pdb=" OD1 ASP D 216 " pdb=" OH TYR D 349 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP E 216 " pdb=" OH TYR E 349 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP B 216 " pdb=" OH TYR B 349 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP C 216 " pdb=" OH TYR C 349 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP F 216 " pdb=" OH TYR F 349 " model vdw 2.255 3.040 ... (remaining 245949 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.27 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 50.320 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.830 ------------------------------------------------------------------------------- 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 : 3.175 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: 0.4018 time to fit residues: 201.6025 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 : 3.389 ------------------------------------------------------------------------------- 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 = 0.136129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103701 restraints weight = 35702.066| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.33 r_work: 0.3145 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1126 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 : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7451 (mtm180) REVERT: C 213 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7838 (mtm180) REVERT: C 289 ASP cc_start: 0.6986 (p0) cc_final: 0.6654 (p0) REVERT: D 134 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8685 (mt-10) REVERT: D 161 TYR cc_start: 0.9148 (m-80) cc_final: 0.8853 (m-80) REVERT: D 213 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7491 (mtm110) REVERT: E 213 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7792 (mtp-110) REVERT: G 213 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7443 (mtm180) REVERT: H 213 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7831 (mtm180) REVERT: H 289 ASP cc_start: 0.6995 (p0) cc_final: 0.6663 (p0) REVERT: I 134 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8682 (mt-10) REVERT: I 161 TYR cc_start: 0.9142 (m-80) cc_final: 0.8848 (m-80) REVERT: I 213 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7502 (mtm110) REVERT: J 213 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7783 (mtp-110) outliers start: 72 outliers final: 32 residues processed: 310 average time/residue: 0.4282 time to fit residues: 208.9154 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 : 2.971 ------------------------------------------------------------------------------- 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: 6.9990 chunk 172 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 226 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 356 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 359 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101618 restraints weight = 35929.196| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.32 r_work: 0.3109 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 28760 Z= 0.311 Angle : 0.596 6.164 39040 Z= 0.311 Chirality : 0.046 0.138 4050 Planarity : 0.005 0.055 5170 Dihedral : 4.246 23.038 4030 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 13.90 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.15), residues: 3640 helix: 1.48 (0.16), residues: 1070 sheet: -0.56 (0.19), residues: 860 loop : 0.32 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 149 HIS 0.004 0.001 HIS D 217 PHE 0.011 0.002 PHE E 68 TYR 0.012 0.001 TYR D 137 ARG 0.002 0.000 ARG I 324 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 1220) hydrogen bonds : angle 5.37666 ( 3270) covalent geometry : bond 0.00747 (28760) covalent geometry : angle 0.59637 (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 330 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 261 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 213 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7504 (mtm180) REVERT: B 214 MET cc_start: 0.8713 (tpp) cc_final: 0.8027 (tpp) REVERT: C 213 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7890 (mtm180) REVERT: D 134 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8831 (mt-10) REVERT: D 213 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7650 (mtm110) REVERT: E 134 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8933 (mt-10) REVERT: E 213 ARG cc_start: 0.8286 (mtp85) cc_final: 0.7906 (mtp-110) REVERT: E 319 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8301 (mmt180) REVERT: G 213 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7445 (mtm110) REVERT: G 214 MET cc_start: 0.8716 (tpp) cc_final: 0.8014 (tpp) REVERT: H 213 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7889 (mtm180) REVERT: I 134 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8837 (mt-10) REVERT: I 213 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7651 (mtm110) REVERT: J 134 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8924 (mt-10) REVERT: J 213 ARG cc_start: 0.8283 (mtp85) cc_final: 0.7905 (mtp-110) REVERT: J 319 ARG cc_start: 0.8510 (mmt180) cc_final: 0.8295 (mmt180) outliers start: 69 outliers final: 39 residues processed: 311 average time/residue: 0.4070 time to fit residues: 198.1514 Evaluate side-chains 289 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 246 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 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: 0.9990 chunk 274 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 133 optimal weight: 8.9990 chunk 273 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.140589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108576 restraints weight = 35298.026| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.33 r_work: 0.3201 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 28760 Z= 0.111 Angle : 0.490 6.097 39040 Z= 0.257 Chirality : 0.041 0.158 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.796 18.176 4030 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.85 % Allowed : 13.36 % Favored : 83.79 % 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: 1.62 (0.16), residues: 1070 sheet: -0.43 (0.19), residues: 820 loop : 0.49 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 130 HIS 0.002 0.001 HIS I 226 PHE 0.009 0.001 PHE E 204 TYR 0.005 0.001 TYR G 349 ARG 0.002 0.000 ARG D 262 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1220) hydrogen bonds : angle 5.08163 ( 3270) covalent geometry : bond 0.00250 (28760) covalent geometry : angle 0.49033 (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 363 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 284 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7661 (mtp) REVERT: A 271 GLU cc_start: 0.8355 (mp0) cc_final: 0.8099 (mp0) REVERT: B 231 ASP cc_start: 0.8874 (m-30) cc_final: 0.8672 (m-30) REVERT: C 13 ILE cc_start: 0.8990 (mm) cc_final: 0.8770 (mt) REVERT: D 17 TYR cc_start: 0.8781 (m-80) cc_final: 0.8453 (m-80) REVERT: D 77 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8096 (mtt) REVERT: D 134 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8820 (mt-10) REVERT: D 161 TYR cc_start: 0.9057 (m-80) cc_final: 0.8754 (m-80) REVERT: D 213 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7377 (mtm110) REVERT: E 134 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8892 (mt-10) REVERT: E 213 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7687 (mtp-110) REVERT: E 319 ARG cc_start: 0.8473 (mmt180) cc_final: 0.8258 (mmt180) REVERT: F 77 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.7661 (mtp) REVERT: F 271 GLU cc_start: 0.8349 (mp0) cc_final: 0.8101 (mp0) REVERT: H 13 ILE cc_start: 0.8996 (mm) cc_final: 0.8777 (mt) REVERT: I 17 TYR cc_start: 0.8783 (m-80) cc_final: 0.8449 (m-80) REVERT: I 77 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8074 (mtt) REVERT: I 134 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8826 (mt-10) REVERT: I 161 TYR cc_start: 0.9054 (m-80) cc_final: 0.8746 (m-80) REVERT: I 213 ARG cc_start: 0.7948 (mtp85) cc_final: 0.7379 (mtm110) REVERT: J 17 TYR cc_start: 0.8773 (m-80) cc_final: 0.8388 (m-80) REVERT: J 134 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8895 (mt-10) REVERT: J 213 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7694 (mtp-110) REVERT: J 319 ARG cc_start: 0.8451 (mmt180) cc_final: 0.8234 (mmt180) outliers start: 79 outliers final: 44 residues processed: 339 average time/residue: 0.3729 time to fit residues: 204.2916 Evaluate side-chains 295 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 243 time to evaluate : 2.930 ------------------------------------------------------------------------------- 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 77 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 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 77 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 328 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Chi-restraints excluded: chain J residue 309 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 70 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 324 optimal weight: 0.8980 chunk 297 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN J 152 ASN J 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109253 restraints weight = 35110.752| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.33 r_work: 0.3214 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28760 Z= 0.110 Angle : 0.480 6.181 39040 Z= 0.248 Chirality : 0.041 0.151 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.670 16.822 4030 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.74 % Allowed : 13.86 % Favored : 83.39 % 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: 0.94 (0.15), residues: 3640 helix: 1.75 (0.16), residues: 1070 sheet: -0.37 (0.19), residues: 800 loop : 0.57 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 130 HIS 0.002 0.000 HIS G 253 PHE 0.009 0.001 PHE D 337 TYR 0.008 0.001 TYR B 349 ARG 0.001 0.000 ARG D 262 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 1220) hydrogen bonds : angle 4.85898 ( 3270) covalent geometry : bond 0.00253 (28760) covalent geometry : angle 0.48001 (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 355 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 279 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.7694 (mtp) REVERT: B 231 ASP cc_start: 0.8838 (m-30) cc_final: 0.8624 (m-30) REVERT: B 267 LEU cc_start: 0.8287 (mt) cc_final: 0.8026 (mt) REVERT: C 13 ILE cc_start: 0.8981 (mm) cc_final: 0.8765 (mt) REVERT: C 309 ILE cc_start: 0.8819 (tt) cc_final: 0.8579 (pt) REVERT: C 349 TYR cc_start: 0.8779 (m-80) cc_final: 0.8555 (m-80) REVERT: D 17 TYR cc_start: 0.8748 (m-80) cc_final: 0.8511 (m-80) REVERT: D 77 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8090 (mtt) REVERT: D 134 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8818 (mt-10) REVERT: D 161 TYR cc_start: 0.9037 (m-80) cc_final: 0.8735 (m-80) REVERT: D 213 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7482 (mtm110) REVERT: D 267 LEU cc_start: 0.7933 (mt) cc_final: 0.7463 (mt) REVERT: D 271 GLU cc_start: 0.8450 (mp0) cc_final: 0.8076 (mp0) REVERT: E 17 TYR cc_start: 0.8797 (m-80) cc_final: 0.8461 (m-80) REVERT: E 134 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8895 (mt-10) REVERT: E 140 MET cc_start: 0.8501 (mtm) cc_final: 0.8265 (mtt) REVERT: E 213 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7687 (mtp-110) REVERT: E 231 ASP cc_start: 0.8896 (m-30) cc_final: 0.8448 (m-30) REVERT: E 319 ARG cc_start: 0.8485 (mmt180) cc_final: 0.8262 (mmt180) REVERT: F 77 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7690 (mtp) REVERT: G 267 LEU cc_start: 0.8294 (mt) cc_final: 0.8034 (mt) REVERT: H 13 ILE cc_start: 0.8990 (mm) cc_final: 0.8772 (mt) REVERT: H 309 ILE cc_start: 0.8813 (tt) cc_final: 0.8573 (pt) REVERT: H 349 TYR cc_start: 0.8775 (m-80) cc_final: 0.8545 (m-80) REVERT: I 17 TYR cc_start: 0.8750 (m-80) cc_final: 0.8507 (m-80) REVERT: I 77 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8074 (mtt) REVERT: I 134 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8823 (mt-10) REVERT: I 161 TYR cc_start: 0.9027 (m-80) cc_final: 0.8724 (m-80) REVERT: I 213 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7480 (mtm110) REVERT: I 267 LEU cc_start: 0.7945 (mt) cc_final: 0.7475 (mt) REVERT: I 271 GLU cc_start: 0.8454 (mp0) cc_final: 0.8079 (mp0) REVERT: J 17 TYR cc_start: 0.8799 (m-80) cc_final: 0.8446 (m-80) REVERT: J 134 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8879 (mt-10) REVERT: J 213 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7683 (mtp-110) REVERT: J 231 ASP cc_start: 0.8891 (m-30) cc_final: 0.8452 (m-30) REVERT: J 319 ARG cc_start: 0.8477 (mmt180) cc_final: 0.8254 (mmt180) outliers start: 76 outliers final: 50 residues processed: 329 average time/residue: 0.3855 time to fit residues: 205.0974 Evaluate side-chains 314 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 256 time to evaluate : 3.053 ------------------------------------------------------------------------------- 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 77 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 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 123 MET 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 77 MET Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 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 123 MET Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 294 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 337 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 G 135 GLN ** 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 = 0.3686 r_free = 0.3686 target = 0.134701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102510 restraints weight = 35851.601| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.31 r_work: 0.3122 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 28760 Z= 0.294 Angle : 0.586 7.579 39040 Z= 0.301 Chirality : 0.045 0.140 4050 Planarity : 0.004 0.054 5170 Dihedral : 4.103 21.541 4030 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.67 % Allowed : 14.77 % Favored : 82.56 % 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: 0.56 (0.15), residues: 3640 helix: 1.48 (0.16), residues: 1070 sheet: -0.70 (0.18), residues: 860 loop : 0.41 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 149 HIS 0.004 0.001 HIS I 217 PHE 0.011 0.002 PHE D 62 TYR 0.011 0.001 TYR D 137 ARG 0.002 0.000 ARG B 227 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 1220) hydrogen bonds : angle 5.09960 ( 3270) covalent geometry : bond 0.00711 (28760) covalent geometry : angle 0.58558 (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 342 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 268 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.7678 (mtp) REVERT: B 213 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7440 (mtm110) REVERT: D 77 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8092 (mtt) REVERT: D 134 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8849 (mt-10) REVERT: D 213 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7637 (mtm110) REVERT: E 134 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8922 (mt-10) REVERT: E 213 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7913 (mtp-110) REVERT: F 77 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7704 (mtp) REVERT: G 213 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7417 (mtm110) REVERT: I 77 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8110 (mtt) REVERT: I 134 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8848 (mt-10) REVERT: I 213 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7623 (mtm110) REVERT: J 134 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8909 (mt-10) REVERT: J 213 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7906 (mtp-110) outliers start: 74 outliers final: 46 residues processed: 309 average time/residue: 0.3970 time to fit residues: 193.9465 Evaluate side-chains 306 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 252 time to evaluate : 3.241 ------------------------------------------------------------------------------- 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 77 MET 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 309 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 77 MET 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 309 ILE Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain 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: 4.9990 chunk 173 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 352 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 244 optimal weight: 0.0970 chunk 270 optimal weight: 0.0980 chunk 140 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ** 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 = 0.3755 r_free = 0.3755 target = 0.140311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108261 restraints weight = 34931.341| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.32 r_work: 0.3206 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28760 Z= 0.117 Angle : 0.491 7.045 39040 Z= 0.253 Chirality : 0.041 0.179 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.794 18.216 4030 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.35 % Allowed : 15.52 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.62 (0.16), residues: 1070 sheet: -0.57 (0.19), residues: 820 loop : 0.48 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 130 HIS 0.002 0.001 HIS J 253 PHE 0.009 0.001 PHE J 204 TYR 0.006 0.001 TYR G 349 ARG 0.002 0.000 ARG D 262 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1220) hydrogen bonds : angle 4.89667 ( 3270) covalent geometry : bond 0.00271 (28760) covalent geometry : angle 0.49081 (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 356 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.7709 (mtp) REVERT: B 231 ASP cc_start: 0.8877 (m-30) cc_final: 0.8648 (m-30) REVERT: C 13 ILE cc_start: 0.9023 (mm) cc_final: 0.8818 (mt) REVERT: C 349 TYR cc_start: 0.8784 (m-80) cc_final: 0.8564 (m-80) REVERT: D 17 TYR cc_start: 0.8785 (m-80) cc_final: 0.8476 (m-80) REVERT: D 77 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8116 (mtt) REVERT: D 134 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8838 (mt-10) REVERT: D 161 TYR cc_start: 0.9091 (m-80) cc_final: 0.8777 (m-80) REVERT: D 213 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7464 (mtm110) REVERT: E 17 TYR cc_start: 0.8794 (m-80) cc_final: 0.8464 (m-80) REVERT: E 213 ARG cc_start: 0.8124 (mtp85) cc_final: 0.7797 (mtp-110) REVERT: E 231 ASP cc_start: 0.8919 (m-30) cc_final: 0.8485 (m-30) REVERT: E 319 ARG cc_start: 0.8483 (mmt180) cc_final: 0.8249 (mmt180) REVERT: F 77 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.7717 (mtp) REVERT: H 349 TYR cc_start: 0.8777 (m-80) cc_final: 0.8551 (m-80) REVERT: I 17 TYR cc_start: 0.8793 (m-80) cc_final: 0.8482 (m-80) REVERT: I 77 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8113 (mtt) REVERT: I 134 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8842 (mt-10) REVERT: I 161 TYR cc_start: 0.9080 (m-80) cc_final: 0.8770 (m-80) REVERT: I 213 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7460 (mtm110) REVERT: J 17 TYR cc_start: 0.8803 (m-80) cc_final: 0.8528 (m-80) REVERT: J 213 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7793 (mtp-110) REVERT: J 231 ASP cc_start: 0.8879 (m-30) cc_final: 0.8455 (m-30) REVERT: J 319 ARG cc_start: 0.8485 (mmt180) cc_final: 0.8253 (mmt180) outliers start: 65 outliers final: 48 residues processed: 337 average time/residue: 0.3998 time to fit residues: 219.6658 Evaluate side-chains 323 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 2.923 ------------------------------------------------------------------------------- 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 77 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain 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 123 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 77 MET 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 197 VAL 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 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 123 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 15 optimal weight: 0.3980 chunk 324 optimal weight: 0.6980 chunk 272 optimal weight: 0.6980 chunk 353 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 333 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN F 194 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 = 0.3762 r_free = 0.3762 target = 0.140408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.108422 restraints weight = 35240.125| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.33 r_work: 0.3205 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28760 Z= 0.121 Angle : 0.495 7.699 39040 Z= 0.253 Chirality : 0.041 0.144 4050 Planarity : 0.004 0.056 5170 Dihedral : 3.704 17.381 4030 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.17 % Allowed : 16.21 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3640 helix: 1.69 (0.16), residues: 1070 sheet: -0.48 (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 F 130 HIS 0.002 0.001 HIS D 253 PHE 0.012 0.001 PHE D 223 TYR 0.008 0.001 TYR B 349 ARG 0.001 0.000 ARG I 262 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 1220) hydrogen bonds : angle 4.81700 ( 3270) covalent geometry : bond 0.00284 (28760) covalent geometry : angle 0.49513 (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 341 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7722 (mtp) REVERT: A 140 MET cc_start: 0.9177 (mtp) cc_final: 0.8938 (mtt) REVERT: B 231 ASP cc_start: 0.8853 (m-30) cc_final: 0.8638 (m-30) REVERT: C 13 ILE cc_start: 0.9025 (mm) cc_final: 0.8811 (mt) REVERT: C 261 MET cc_start: 0.8678 (ttm) cc_final: 0.8431 (ttm) REVERT: D 17 TYR cc_start: 0.8733 (m-80) cc_final: 0.8403 (m-80) REVERT: D 77 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: D 84 MET cc_start: 0.8409 (tpp) cc_final: 0.8180 (ttm) REVERT: D 134 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8831 (mt-10) REVERT: D 161 TYR cc_start: 0.9087 (m-80) cc_final: 0.8779 (m-80) REVERT: D 213 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7505 (mtm110) REVERT: E 17 TYR cc_start: 0.8825 (m-80) cc_final: 0.8497 (m-80) REVERT: E 213 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7782 (mtp-110) REVERT: E 231 ASP cc_start: 0.8909 (m-30) cc_final: 0.8455 (m-30) REVERT: E 319 ARG cc_start: 0.8504 (mmt180) cc_final: 0.8266 (mmt180) REVERT: F 77 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7723 (mtp) REVERT: F 140 MET cc_start: 0.9182 (mtp) cc_final: 0.8942 (mtt) REVERT: H 13 ILE cc_start: 0.9032 (mm) cc_final: 0.8825 (mt) REVERT: H 261 MET cc_start: 0.8678 (ttm) cc_final: 0.8432 (ttm) REVERT: I 17 TYR cc_start: 0.8769 (m-80) cc_final: 0.8512 (m-80) REVERT: I 77 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8063 (mtt) REVERT: I 84 MET cc_start: 0.8435 (tpp) cc_final: 0.8205 (ttm) REVERT: I 134 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8827 (mt-10) REVERT: I 161 TYR cc_start: 0.9067 (m-80) cc_final: 0.8756 (m-80) REVERT: I 213 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7499 (mtm110) REVERT: J 17 TYR cc_start: 0.8831 (m-80) cc_final: 0.8489 (m-80) REVERT: J 213 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7777 (mtp-110) REVERT: J 231 ASP cc_start: 0.8899 (m-30) cc_final: 0.8450 (m-30) REVERT: J 319 ARG cc_start: 0.8500 (mmt180) cc_final: 0.8260 (mmt180) outliers start: 60 outliers final: 48 residues processed: 326 average time/residue: 0.3965 time to fit residues: 209.5846 Evaluate side-chains 323 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 3.477 ------------------------------------------------------------------------------- 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 77 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain 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 123 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 77 MET 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 197 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain 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 123 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 173 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 chunk 293 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 349 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.139365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107547 restraints weight = 35437.729| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.32 r_work: 0.3196 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 28760 Z= 0.148 Angle : 0.508 7.617 39040 Z= 0.259 Chirality : 0.042 0.141 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.759 17.770 4030 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.17 % Allowed : 16.17 % Favored : 81.66 % 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: 0.77 (0.15), residues: 3640 helix: 1.66 (0.16), residues: 1070 sheet: -0.59 (0.19), residues: 820 loop : 0.52 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 32 HIS 0.002 0.001 HIS A 8 PHE 0.011 0.001 PHE D 223 TYR 0.007 0.001 TYR B 137 ARG 0.001 0.000 ARG I 357 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1220) hydrogen bonds : angle 4.82911 ( 3270) covalent geometry : bond 0.00355 (28760) covalent geometry : angle 0.50760 (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 334 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 274 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7727 (mtp) REVERT: A 140 MET cc_start: 0.9194 (mtp) cc_final: 0.8964 (mtt) REVERT: C 261 MET cc_start: 0.8570 (ttm) cc_final: 0.8329 (ttm) REVERT: D 17 TYR cc_start: 0.8707 (m-80) cc_final: 0.8398 (m-80) REVERT: D 77 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8070 (mtt) REVERT: D 134 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8807 (mt-10) REVERT: D 161 TYR cc_start: 0.9117 (m-80) cc_final: 0.8808 (m-80) REVERT: D 213 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7513 (mtm110) REVERT: E 213 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7793 (mtp-110) REVERT: E 231 ASP cc_start: 0.8924 (m-30) cc_final: 0.8546 (m-30) REVERT: E 319 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8271 (mmt180) REVERT: F 77 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.7724 (mtp) REVERT: F 140 MET cc_start: 0.9199 (mtp) cc_final: 0.8967 (mtt) REVERT: H 261 MET cc_start: 0.8571 (ttm) cc_final: 0.8327 (ttm) REVERT: I 17 TYR cc_start: 0.8787 (m-80) cc_final: 0.8495 (m-80) REVERT: I 77 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8086 (mtt) REVERT: I 134 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8807 (mt-10) REVERT: I 161 TYR cc_start: 0.9097 (m-80) cc_final: 0.8780 (m-80) REVERT: I 213 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7517 (mtm110) REVERT: J 213 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7787 (mtp-110) REVERT: J 231 ASP cc_start: 0.8902 (m-30) cc_final: 0.8474 (m-30) REVERT: J 319 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8268 (mmt180) outliers start: 60 outliers final: 49 residues processed: 319 average time/residue: 0.3822 time to fit residues: 196.0727 Evaluate side-chains 316 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 2.967 ------------------------------------------------------------------------------- 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 77 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain 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 123 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 77 MET 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 197 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 334 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 339 optimal weight: 0.4980 chunk 289 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.107153 restraints weight = 35243.784| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.32 r_work: 0.3194 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28760 Z= 0.154 Angle : 0.521 8.411 39040 Z= 0.267 Chirality : 0.042 0.174 4050 Planarity : 0.004 0.055 5170 Dihedral : 3.780 17.875 4030 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.02 % Allowed : 16.43 % Favored : 81.55 % 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: 1.59 (0.16), residues: 1070 sheet: -0.59 (0.19), residues: 820 loop : 0.52 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 32 HIS 0.002 0.001 HIS B 217 PHE 0.011 0.001 PHE I 223 TYR 0.008 0.001 TYR G 349 ARG 0.002 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 1220) hydrogen bonds : angle 4.90006 ( 3270) covalent geometry : bond 0.00366 (28760) covalent geometry : angle 0.52120 (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 328 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7715 (mtp) REVERT: A 140 MET cc_start: 0.9187 (mtp) cc_final: 0.8956 (mtt) REVERT: C 13 ILE cc_start: 0.9036 (mm) cc_final: 0.8815 (mt) REVERT: C 47 LEU cc_start: 0.8357 (tp) cc_final: 0.8007 (tp) REVERT: C 261 MET cc_start: 0.8620 (ttm) cc_final: 0.8411 (ttm) REVERT: C 349 TYR cc_start: 0.8764 (m-80) cc_final: 0.8506 (m-80) REVERT: D 17 TYR cc_start: 0.8704 (m-80) cc_final: 0.8386 (m-80) REVERT: D 77 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8109 (mtt) REVERT: D 134 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8807 (mt-10) REVERT: D 140 MET cc_start: 0.9329 (mtp) cc_final: 0.9004 (mmm) REVERT: D 161 TYR cc_start: 0.9116 (m-80) cc_final: 0.8805 (m-80) REVERT: D 213 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7523 (mtm110) REVERT: E 213 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7791 (mtp-110) REVERT: E 231 ASP cc_start: 0.8933 (m-30) cc_final: 0.8498 (m-30) REVERT: E 319 ARG cc_start: 0.8499 (mmt180) cc_final: 0.8257 (mmt180) REVERT: F 77 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7721 (mtp) REVERT: F 140 MET cc_start: 0.9190 (mtp) cc_final: 0.8958 (mtt) REVERT: H 47 LEU cc_start: 0.8352 (tp) cc_final: 0.7998 (tp) REVERT: H 261 MET cc_start: 0.8625 (ttm) cc_final: 0.8417 (ttm) REVERT: H 349 TYR cc_start: 0.8757 (m-80) cc_final: 0.8493 (m-80) REVERT: I 17 TYR cc_start: 0.8789 (m-80) cc_final: 0.8486 (m-80) REVERT: I 77 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8075 (mtt) REVERT: I 134 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8804 (mt-10) REVERT: I 140 MET cc_start: 0.9310 (mtp) cc_final: 0.8985 (mmm) REVERT: I 161 TYR cc_start: 0.9097 (m-80) cc_final: 0.8771 (m-80) REVERT: I 213 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7522 (mtm110) REVERT: J 213 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7793 (mtp-110) REVERT: J 319 ARG cc_start: 0.8512 (mmt180) cc_final: 0.8270 (mmt180) outliers start: 56 outliers final: 50 residues processed: 316 average time/residue: 0.3870 time to fit residues: 196.3470 Evaluate side-chains 326 residues out of total 3100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 2.992 ------------------------------------------------------------------------------- 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 77 MET Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 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 197 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 77 MET 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 197 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 123 optimal weight: 6.9990 chunk 286 optimal weight: 0.6980 chunk 262 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 345 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 132 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 ASN F 152 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110977 restraints weight = 35233.513| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.33 r_work: 0.3239 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28760 Z= 0.103 Angle : 0.495 8.013 39040 Z= 0.253 Chirality : 0.041 0.185 4050 Planarity : 0.004 0.058 5170 Dihedral : 3.589 16.071 4030 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.95 % Allowed : 16.61 % Favored : 81.44 % 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: 0.91 (0.15), residues: 3640 helix: 1.72 (0.16), residues: 1070 sheet: -0.44 (0.20), residues: 800 loop : 0.59 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 130 HIS 0.003 0.000 HIS F 253 PHE 0.013 0.001 PHE D 256 TYR 0.008 0.001 TYR B 349 ARG 0.006 0.000 ARG F 213 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 1220) hydrogen bonds : angle 4.78257 ( 3270) covalent geometry : bond 0.00236 (28760) covalent geometry : angle 0.49457 (39040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12765.50 seconds wall clock time: 222 minutes 7.51 seconds (13327.51 seconds total)