Starting phenix.real_space_refine on Thu Feb 5 17:44:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h2s_51817/02_2026/9h2s_51817_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h2s_51817/02_2026/9h2s_51817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9h2s_51817/02_2026/9h2s_51817_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h2s_51817/02_2026/9h2s_51817_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9h2s_51817/02_2026/9h2s_51817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h2s_51817/02_2026/9h2s_51817.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 11963 2.51 5 N 3073 2.21 5 O 3143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18235 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "D" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "E" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "F" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "G" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2569 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'D12': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.02, per 1000 atoms: 0.22 Number of scatterers: 18235 At special positions: 0 Unit cell: (122.034, 122.98, 148.522, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3143 8.00 N 3073 7.00 C 11963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 832.7 milliseconds 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4242 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 9 sheets defined 59.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 32 removed outlier: 3.663A pdb=" N ASN A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU A 11 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 134 removed outlier: 3.615A pdb=" N MET A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 294 through 314 Processing helix chain 'D' and resid 5 through 32 removed outlier: 3.663A pdb=" N ASN D 9 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D 11 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 24 " --> pdb=" O CYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE D 78 " --> pdb=" O THR D 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 134 removed outlier: 3.616A pdb=" N MET D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 160 Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 294 through 314 Processing helix chain 'B' and resid 5 through 32 removed outlier: 3.663A pdb=" N ASN B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU B 11 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 24 " --> pdb=" O CYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 109 removed outlier: 3.691A pdb=" N ILE B 78 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 134 removed outlier: 3.615A pdb=" N MET B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 160 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 294 through 314 Processing helix chain 'C' and resid 5 through 32 removed outlier: 3.662A pdb=" N ASN C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 24 " --> pdb=" O CYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 134 removed outlier: 3.616A pdb=" N MET C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 160 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 294 through 314 Processing helix chain 'E' and resid 5 through 32 removed outlier: 3.663A pdb=" N ASN E 9 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU E 11 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE E 24 " --> pdb=" O CYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 134 removed outlier: 3.616A pdb=" N MET E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 160 Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 246 through 260 Processing helix chain 'E' and resid 294 through 314 Processing helix chain 'F' and resid 5 through 32 removed outlier: 3.662A pdb=" N ASN F 9 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU F 11 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN F 12 " --> pdb=" O ASN F 8 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 24 " --> pdb=" O CYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE F 78 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU F 97 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 134 removed outlier: 3.615A pdb=" N MET F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 160 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 216 through 221 Processing helix chain 'F' and resid 246 through 260 Processing helix chain 'F' and resid 294 through 314 Processing helix chain 'G' and resid 5 through 32 removed outlier: 3.662A pdb=" N ASN G 9 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN G 12 " --> pdb=" O ASN G 8 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 24 " --> pdb=" O CYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 68 removed outlier: 3.658A pdb=" N ILE G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE G 53 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 109 removed outlier: 3.692A pdb=" N ILE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU G 97 " --> pdb=" O LYS G 93 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 134 removed outlier: 3.616A pdb=" N MET G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 160 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 216 through 221 Processing helix chain 'G' and resid 246 through 260 Processing helix chain 'G' and resid 294 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.566A pdb=" N VAL A 185 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 203 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL A 197 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G 185 " --> pdb=" O GLY G 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR G 203 " --> pdb=" O LEU G 195 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL G 197 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER G 201 " --> pdb=" O VAL G 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 185 " --> pdb=" O GLY F 192 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR F 203 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL F 197 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER F 201 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 185 " --> pdb=" O GLY E 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR E 203 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL E 197 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 185 " --> pdb=" O GLY D 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR D 203 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL D 197 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N SER D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 185 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR C 203 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL C 197 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 185 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR B 203 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL B 197 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN A 283 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 327 removed outlier: 8.374A pdb=" N MET B 322 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASP A 323 " --> pdb=" O MET B 322 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B 324 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN A 325 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE B 326 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LYS A 327 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N MET C 322 " --> pdb=" O GLN B 321 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 323 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 324 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN B 325 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE C 326 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS B 327 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET E 322 " --> pdb=" O GLN D 321 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP D 323 " --> pdb=" O MET E 322 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL E 324 " --> pdb=" O ASP D 323 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASN D 325 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE E 326 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS D 327 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N MET F 322 " --> pdb=" O GLN E 321 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP E 323 " --> pdb=" O MET F 322 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL F 324 " --> pdb=" O ASP E 323 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN E 325 " --> pdb=" O VAL F 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE F 326 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS E 327 " --> pdb=" O PHE F 326 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N MET G 322 " --> pdb=" O GLN F 321 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP F 323 " --> pdb=" O MET G 322 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL G 324 " --> pdb=" O ASP F 323 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASN F 325 " --> pdb=" O VAL G 324 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE G 326 " --> pdb=" O ASN F 325 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LYS F 327 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN D 283 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN B 283 " --> pdb=" O ASN B 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN C 283 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 232 through 241 removed outlier: 6.627A pdb=" N ASN E 283 " --> pdb=" O ASN E 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN F 283 " --> pdb=" O ASN F 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 232 through 241 removed outlier: 6.628A pdb=" N ASN G 283 " --> pdb=" O ASN G 275 " (cutoff:3.500A) 1256 hydrogen bonds defined for protein. 3684 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: 3.20 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4440 1.33 - 1.45: 3241 1.45 - 1.57: 10729 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 18508 Sorted by residual: bond pdb=" C ILE B 60 " pdb=" O ILE B 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.09e+00 bond pdb=" C ILE G 60 " pdb=" O ILE G 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.07e+00 bond pdb=" C ILE C 60 " pdb=" O ILE C 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.02e+00 bond pdb=" C ILE A 60 " pdb=" O ILE A 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.02e+00 bond pdb=" C ILE D 60 " pdb=" O ILE D 60 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.19e-02 7.06e+03 4.01e+00 ... (remaining 18503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 24381 1.53 - 3.05: 460 3.05 - 4.58: 65 4.58 - 6.10: 14 6.10 - 7.63: 14 Bond angle restraints: 24934 Sorted by residual: angle pdb=" N GLY B 58 " pdb=" CA GLY B 58 " pdb=" C GLY B 58 " ideal model delta sigma weight residual 112.49 104.86 7.63 1.21e+00 6.83e-01 3.97e+01 angle pdb=" N GLY E 58 " pdb=" CA GLY E 58 " pdb=" C GLY E 58 " ideal model delta sigma weight residual 112.49 104.90 7.59 1.21e+00 6.83e-01 3.93e+01 angle pdb=" N GLY A 58 " pdb=" CA GLY A 58 " pdb=" C GLY A 58 " ideal model delta sigma weight residual 112.49 104.91 7.58 1.21e+00 6.83e-01 3.93e+01 angle pdb=" N GLY C 58 " pdb=" CA GLY C 58 " pdb=" C GLY C 58 " ideal model delta sigma weight residual 112.49 104.92 7.57 1.21e+00 6.83e-01 3.92e+01 angle pdb=" N GLY D 58 " pdb=" CA GLY D 58 " pdb=" C GLY D 58 " ideal model delta sigma weight residual 112.49 104.92 7.57 1.21e+00 6.83e-01 3.92e+01 ... (remaining 24929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 9660 17.57 - 35.14: 1057 35.14 - 52.71: 336 52.71 - 70.28: 7 70.28 - 87.86: 28 Dihedral angle restraints: 11088 sinusoidal: 4508 harmonic: 6580 Sorted by residual: dihedral pdb=" CG LYS B 327 " pdb=" CD LYS B 327 " pdb=" CE LYS B 327 " pdb=" NZ LYS B 327 " ideal model delta sinusoidal sigma weight residual -60.00 -113.83 53.83 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CG LYS C 327 " pdb=" CD LYS C 327 " pdb=" CE LYS C 327 " pdb=" NZ LYS C 327 " ideal model delta sinusoidal sigma weight residual -60.00 -113.81 53.81 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CG LYS F 327 " pdb=" CD LYS F 327 " pdb=" CE LYS F 327 " pdb=" NZ LYS F 327 " ideal model delta sinusoidal sigma weight residual -60.00 -113.79 53.79 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 11085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1917 0.025 - 0.050: 508 0.050 - 0.075: 291 0.075 - 0.099: 153 0.099 - 0.124: 99 Chirality restraints: 2968 Sorted by residual: chirality pdb=" CA VAL E 64 " pdb=" N VAL E 64 " pdb=" C VAL E 64 " pdb=" CB VAL E 64 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL C 64 " pdb=" N VAL C 64 " pdb=" C VAL C 64 " pdb=" CB VAL C 64 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL B 64 " pdb=" N VAL B 64 " pdb=" C VAL B 64 " pdb=" CB VAL B 64 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 2965 not shown) Planarity restraints: 3087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 56 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C ALA D 56 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA D 56 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL D 57 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 56 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ALA G 56 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA G 56 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL G 57 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 56 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.03e+00 pdb=" C ALA B 56 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA B 56 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 57 " -0.008 2.00e-02 2.50e+03 ... (remaining 3084 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 98 2.57 - 3.15: 15876 3.15 - 3.74: 27583 3.74 - 4.32: 37856 4.32 - 4.90: 64884 Nonbonded interactions: 146297 Sorted by model distance: nonbonded pdb=" N GLU G 136 " pdb=" OE1 GLU G 136 " model vdw 1.990 3.120 nonbonded pdb=" N GLU C 136 " pdb=" OE1 GLU C 136 " model vdw 1.990 3.120 nonbonded pdb=" N GLU E 136 " pdb=" OE1 GLU E 136 " model vdw 1.990 3.120 nonbonded pdb=" N GLU D 136 " pdb=" OE1 GLU D 136 " model vdw 1.990 3.120 nonbonded pdb=" N GLU A 136 " pdb=" OE1 GLU A 136 " model vdw 1.990 3.120 ... (remaining 146292 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 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 : 0.003 0.024 18508 Z= 0.159 Angle : 0.521 7.626 24934 Z= 0.370 Chirality : 0.038 0.124 2968 Planarity : 0.002 0.014 3087 Dihedral : 15.781 87.856 6846 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.84 % Allowed : 28.62 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.19), residues: 2275 helix: 2.72 (0.15), residues: 1344 sheet: 0.02 (0.31), residues: 245 loop : -2.01 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 234 TYR 0.005 0.001 TYR E 299 PHE 0.017 0.001 PHE F 101 TRP 0.002 0.000 TRP E 289 HIS 0.002 0.000 HIS E 137 Details of bonding type rmsd covalent geometry : bond 0.00266 (18508) covalent geometry : angle 0.52116 (24934) hydrogen bonds : bond 0.20933 ( 1256) hydrogen bonds : angle 7.26447 ( 3684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.625 Fit side-chains REVERT: A 60 ILE cc_start: 0.5136 (OUTLIER) cc_final: 0.4851 (tt) REVERT: D 60 ILE cc_start: 0.5379 (OUTLIER) cc_final: 0.5174 (tt) REVERT: D 80 PHE cc_start: 0.6917 (t80) cc_final: 0.6715 (t80) REVERT: D 116 ARG cc_start: 0.7484 (tpp-160) cc_final: 0.7252 (ttm110) REVERT: D 183 GLU cc_start: 0.8396 (tt0) cc_final: 0.7940 (tt0) REVERT: B 60 ILE cc_start: 0.5030 (OUTLIER) cc_final: 0.4735 (tt) REVERT: B 183 GLU cc_start: 0.8333 (tt0) cc_final: 0.7908 (tt0) REVERT: C 60 ILE cc_start: 0.5556 (OUTLIER) cc_final: 0.5304 (tt) REVERT: C 328 ARG cc_start: 0.6693 (mmm160) cc_final: 0.6464 (ttm-80) REVERT: E 60 ILE cc_start: 0.5490 (OUTLIER) cc_final: 0.5268 (tt) REVERT: E 116 ARG cc_start: 0.7477 (tpp-160) cc_final: 0.7272 (ttm110) REVERT: E 183 GLU cc_start: 0.8490 (tt0) cc_final: 0.7982 (tt0) REVERT: E 276 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: F 60 ILE cc_start: 0.5649 (OUTLIER) cc_final: 0.5439 (tt) REVERT: F 183 GLU cc_start: 0.8650 (tt0) cc_final: 0.8263 (tt0) REVERT: G 60 ILE cc_start: 0.5142 (OUTLIER) cc_final: 0.4871 (tt) outliers start: 36 outliers final: 7 residues processed: 242 average time/residue: 0.5078 time to fit residues: 139.4640 Evaluate side-chains 210 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 122 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 141 GLN D 137 HIS D 283 ASN B 137 HIS B 235 ASN C 137 HIS E 137 HIS E 141 GLN E 235 ASN E 283 ASN F 137 HIS F 141 GLN F 283 ASN G 137 HIS G 141 GLN G 283 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.185314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103198 restraints weight = 25403.978| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.26 r_work: 0.3426 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 18508 Z= 0.288 Angle : 0.598 7.717 24934 Z= 0.323 Chirality : 0.045 0.200 2968 Planarity : 0.004 0.024 3087 Dihedral : 5.430 57.997 2698 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 6.76 % Allowed : 23.35 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.17), residues: 2275 helix: 1.92 (0.14), residues: 1372 sheet: 1.07 (0.31), residues: 238 loop : -1.61 (0.21), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 180 TYR 0.011 0.001 TYR A 134 PHE 0.014 0.001 PHE E 237 TRP 0.009 0.001 TRP D 29 HIS 0.004 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00711 (18508) covalent geometry : angle 0.59787 (24934) hydrogen bonds : bond 0.05738 ( 1256) hydrogen bonds : angle 4.65118 ( 3684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 230 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.4903 (OUTLIER) cc_final: 0.4493 (t0) REVERT: A 96 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7383 (tm) REVERT: A 204 MET cc_start: 0.8961 (ptm) cc_final: 0.8689 (ptp) REVERT: D 12 ASN cc_start: 0.5252 (OUTLIER) cc_final: 0.4930 (t0) REVERT: D 80 PHE cc_start: 0.6914 (t80) cc_final: 0.6692 (t80) REVERT: B 12 ASN cc_start: 0.4840 (OUTLIER) cc_final: 0.4393 (t0) REVERT: B 183 GLU cc_start: 0.8755 (tt0) cc_final: 0.8522 (tt0) REVERT: C 12 ASN cc_start: 0.5125 (OUTLIER) cc_final: 0.4783 (t0) REVERT: C 137 HIS cc_start: 0.5362 (m90) cc_final: 0.5135 (m-70) REVERT: C 273 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7812 (ptm160) REVERT: E 96 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7657 (tm) REVERT: E 190 VAL cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (m) REVERT: F 12 ASN cc_start: 0.4783 (OUTLIER) cc_final: 0.4547 (t0) REVERT: F 96 LEU cc_start: 0.7810 (mm) cc_final: 0.7530 (tp) REVERT: F 190 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8089 (m) REVERT: G 12 ASN cc_start: 0.4482 (OUTLIER) cc_final: 0.4099 (t0) REVERT: G 96 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7347 (tp) REVERT: G 183 GLU cc_start: 0.8910 (tt0) cc_final: 0.8629 (tt0) REVERT: G 190 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8029 (m) outliers start: 132 outliers final: 48 residues processed: 339 average time/residue: 0.5175 time to fit residues: 199.4236 Evaluate side-chains 280 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 273 ARG Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 200 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 235 ASN D 137 HIS D 235 ASN B 137 HIS C 235 ASN E 137 HIS F 137 HIS G 235 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.206168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.124531 restraints weight = 25382.569| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.15 r_work: 0.3508 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18508 Z= 0.143 Angle : 0.503 7.986 24934 Z= 0.262 Chirality : 0.041 0.138 2968 Planarity : 0.003 0.025 3087 Dihedral : 5.003 59.919 2681 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 7.22 % Allowed : 22.17 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.17), residues: 2275 helix: 1.86 (0.14), residues: 1372 sheet: 1.21 (0.30), residues: 238 loop : -1.11 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 116 TYR 0.009 0.001 TYR C 134 PHE 0.009 0.001 PHE G 326 TRP 0.005 0.001 TRP C 29 HIS 0.003 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00340 (18508) covalent geometry : angle 0.50331 (24934) hydrogen bonds : bond 0.04333 ( 1256) hydrogen bonds : angle 4.01924 ( 3684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 227 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.4679 (OUTLIER) cc_final: 0.4362 (t0) REVERT: A 96 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7482 (tm) REVERT: A 273 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6992 (ptm160) REVERT: D 12 ASN cc_start: 0.5065 (OUTLIER) cc_final: 0.4829 (t0) REVERT: D 116 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7294 (ttm170) REVERT: D 273 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7719 (ptm160) REVERT: D 326 PHE cc_start: 0.7362 (m-10) cc_final: 0.7060 (m-80) REVERT: B 12 ASN cc_start: 0.4931 (OUTLIER) cc_final: 0.4542 (t0) REVERT: B 183 GLU cc_start: 0.8653 (tt0) cc_final: 0.8414 (tt0) REVERT: C 12 ASN cc_start: 0.4961 (OUTLIER) cc_final: 0.4575 (t0) REVERT: C 116 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7308 (ttm170) REVERT: C 273 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7616 (ptm160) REVERT: E 26 MET cc_start: 0.1677 (mmp) cc_final: 0.1255 (mmm) REVERT: E 190 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8163 (m) REVERT: E 309 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7957 (mm-30) REVERT: F 12 ASN cc_start: 0.4808 (OUTLIER) cc_final: 0.4381 (t0) REVERT: F 96 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7587 (tm) REVERT: F 137 HIS cc_start: 0.5180 (m90) cc_final: 0.4843 (m-70) REVERT: F 190 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8095 (m) REVERT: G 12 ASN cc_start: 0.4583 (OUTLIER) cc_final: 0.4196 (t0) REVERT: G 96 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7407 (tm) REVERT: G 116 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7286 (ttm170) REVERT: G 183 GLU cc_start: 0.8646 (tt0) cc_final: 0.8291 (tt0) REVERT: G 190 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8020 (m) REVERT: G 273 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6849 (ptm160) outliers start: 141 outliers final: 47 residues processed: 339 average time/residue: 0.5023 time to fit residues: 192.6764 Evaluate side-chains 279 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 216 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 173 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 chunk 71 optimal weight: 0.0030 chunk 73 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 134 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 overall best weight: 3.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS D 43 HIS D 137 HIS B 137 HIS B 283 ASN C 137 HIS C 141 GLN E 43 HIS E 137 HIS F 141 GLN G 100 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.181309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101376 restraints weight = 24973.477| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.28 r_work: 0.3221 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 18508 Z= 0.302 Angle : 0.608 8.713 24934 Z= 0.315 Chirality : 0.044 0.176 2968 Planarity : 0.004 0.028 3087 Dihedral : 5.263 59.716 2677 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 7.07 % Allowed : 22.02 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2275 helix: 1.76 (0.14), residues: 1372 sheet: 0.52 (0.28), residues: 280 loop : -1.01 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.009 0.001 TYR F 299 PHE 0.017 0.001 PHE G 237 TRP 0.006 0.001 TRP G 289 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00747 (18508) covalent geometry : angle 0.60831 (24934) hydrogen bonds : bond 0.04958 ( 1256) hydrogen bonds : angle 4.08029 ( 3684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4550 Ramachandran restraints generated. 2275 Oldfield, 0 Emsley, 2275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 219 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.4328 (OUTLIER) cc_final: 0.3982 (t0) REVERT: A 96 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7452 (tm) REVERT: D 269 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7255 (pp20) REVERT: B 12 ASN cc_start: 0.4538 (OUTLIER) cc_final: 0.4207 (t0) REVERT: C 12 ASN cc_start: 0.4727 (OUTLIER) cc_final: 0.4316 (t0) REVERT: C 269 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7997 (pp20) REVERT: C 273 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7724 (ptm160) REVERT: E 26 MET cc_start: 0.1418 (mmp) cc_final: 0.1058 (mmm) REVERT: E 190 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8142 (m) REVERT: F 12 ASN cc_start: 0.4282 (OUTLIER) cc_final: 0.3980 (t0) REVERT: F 96 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7483 (tm) REVERT: F 190 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8038 (m) REVERT: G 12 ASN cc_start: 0.4108 (OUTLIER) cc_final: 0.3820 (t0) REVERT: G 96 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7431 (tm) REVERT: G 183 GLU cc_start: 0.8736 (tt0) cc_final: 0.8263 (tt0) REVERT: G 190 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.8007 (m) outliers start: 138 outliers final: 66 residues processed: 327 average time/residue: 0.5417 time to fit residues: 200.7884 Evaluate side-chains 287 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 207 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 267 ASP Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 273 ARG Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 72 PHE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 273 ARG Chi-restraints excluded: chain F residue 292 SER Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 267 ASP Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 273 ARG Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1227 > 50: distance: 17 - 23: 12.468 distance: 23 - 24: 11.224 distance: 24 - 25: 27.629 distance: 24 - 27: 8.799 distance: 25 - 26: 19.750 distance: 25 - 34: 16.883 distance: 27 - 28: 11.634 distance: 28 - 29: 21.454 distance: 28 - 30: 24.927 distance: 29 - 31: 9.673 distance: 30 - 32: 14.641 distance: 31 - 33: 11.776 distance: 32 - 33: 36.503 distance: 34 - 35: 12.087 distance: 35 - 36: 21.125 distance: 35 - 38: 36.863 distance: 36 - 37: 22.649 distance: 36 - 42: 16.940 distance: 38 - 39: 26.203 distance: 38 - 40: 28.978 distance: 39 - 41: 13.125 distance: 42 - 43: 11.789 distance: 43 - 44: 4.347 distance: 43 - 46: 28.772 distance: 44 - 45: 22.888 distance: 44 - 49: 18.625 distance: 46 - 47: 16.264 distance: 46 - 48: 38.727 distance: 49 - 50: 30.921 distance: 49 - 55: 14.320 distance: 50 - 51: 14.930 distance: 50 - 53: 17.810 distance: 51 - 52: 13.060 distance: 51 - 56: 11.133 distance: 52 - 75: 18.860 distance: 53 - 54: 17.834 distance: 54 - 55: 12.172 distance: 56 - 57: 15.665 distance: 57 - 58: 13.317 distance: 58 - 59: 11.302 distance: 58 - 60: 11.561 distance: 59 - 83: 3.644 distance: 60 - 61: 9.316 distance: 61 - 62: 13.487 distance: 61 - 64: 19.395 distance: 62 - 63: 7.766 distance: 62 - 67: 4.536 distance: 63 - 94: 3.675 distance: 64 - 65: 6.309 distance: 64 - 66: 7.788 distance: 67 - 68: 7.808 distance: 68 - 69: 9.622 distance: 68 - 71: 13.949 distance: 69 - 70: 11.872 distance: 69 - 75: 6.752 distance: 70 - 102: 10.880 distance: 71 - 72: 8.611 distance: 71 - 73: 14.155 distance: 72 - 74: 10.008 distance: 75 - 76: 10.495 distance: 76 - 77: 11.246 distance: 76 - 79: 12.063 distance: 77 - 78: 14.219 distance: 77 - 83: 12.309 distance: 78 - 108: 10.252 distance: 79 - 80: 8.076 distance: 80 - 81: 4.737 distance: 80 - 82: 12.622 distance: 83 - 84: 4.768 distance: 84 - 85: 10.136 distance: 84 - 87: 10.495 distance: 85 - 86: 8.862 distance: 85 - 94: 7.234 distance: 86 - 115: 12.163 distance: 87 - 88: 13.572 distance: 88 - 89: 20.212 distance: 89 - 91: 11.175 distance: 90 - 92: 18.075 distance: 91 - 93: 10.008 distance: 92 - 93: 16.220 distance: 94 - 95: 5.188 distance: 95 - 96: 6.851 distance: 95 - 98: 13.687 distance: 96 - 97: 10.088 distance: 96 - 102: 3.129 distance: 97 - 121: 11.790 distance: 98 - 99: 8.558 distance: 98 - 100: 15.744 distance: 99 - 101: 26.372