Starting phenix.real_space_refine on Wed Mar 4 17:36:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2u_15107/03_2026/8a2u_15107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2u_15107/03_2026/8a2u_15107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2u_15107/03_2026/8a2u_15107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2u_15107/03_2026/8a2u_15107.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2u_15107/03_2026/8a2u_15107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2u_15107/03_2026/8a2u_15107.cif" } resolution = 2.21 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= 0.007 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: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 10 5.49 5 S 100 5.16 5 Be 5 3.05 5 C 9145 2.51 5 N 2445 2.21 5 O 3297 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15022 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' CA': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "D" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Time building chain proxies: 3.89, per 1000 atoms: 0.26 Number of scatterers: 15022 At special positions: 0 Unit cell: (93.825, 89.655, 192.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 S 100 16.00 P 10 15.00 F 15 9.00 O 3297 8.00 N 2445 7.00 C 9145 6.00 Be 5 4.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 692.4 milliseconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 50.5% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.520A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.692A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.733A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.236A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.580A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 93 removed outlier: 3.520A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.692A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.733A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.236A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.579A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.519A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.692A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.732A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.236A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.579A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.520A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.692A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.971A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.733A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.235A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.579A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.520A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.691A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.970A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.733A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.235A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.580A pdb=" N GLU E 364 " --> pdb=" O GLN E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.565A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.870A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.870A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.281A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.773A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.565A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.564A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.280A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.832A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.564A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.280A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.565A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.280A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 698 hydrogen bonds defined for protein. 1788 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: 3.02 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4702 1.34 - 1.46: 3040 1.46 - 1.58: 6888 1.58 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14820 Sorted by residual: bond pdb=" F2 BEF B 403 " pdb="BE BEF B 403 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" F2 BEF A 403 " pdb="BE BEF A 403 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" F2 BEF E 403 " pdb="BE BEF E 403 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" F2 BEF D 403 " pdb="BE BEF D 403 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" F2 BEF C 403 " pdb="BE BEF C 403 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 14815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 19893 2.67 - 5.33: 177 5.33 - 8.00: 20 8.00 - 10.66: 10 10.66 - 13.33: 5 Bond angle restraints: 20105 Sorted by residual: angle pdb=" F2 BEF A 403 " pdb="BE BEF A 403 " pdb=" F3 BEF A 403 " ideal model delta sigma weight residual 119.96 106.63 13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" F2 BEF E 403 " pdb="BE BEF E 403 " pdb=" F3 BEF E 403 " ideal model delta sigma weight residual 119.96 106.63 13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" F2 BEF B 403 " pdb="BE BEF B 403 " pdb=" F3 BEF B 403 " ideal model delta sigma weight residual 119.96 106.64 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" F2 BEF C 403 " pdb="BE BEF C 403 " pdb=" F3 BEF C 403 " ideal model delta sigma weight residual 119.96 106.64 13.32 3.00e+00 1.11e-01 1.97e+01 angle pdb=" F2 BEF D 403 " pdb="BE BEF D 403 " pdb=" F3 BEF D 403 " ideal model delta sigma weight residual 119.96 106.67 13.29 3.00e+00 1.11e-01 1.96e+01 ... (remaining 20100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.33: 8735 30.33 - 60.66: 140 60.66 - 91.00: 25 91.00 - 121.33: 0 121.33 - 151.66: 10 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.66 -151.66 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.64 -151.64 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 91.63 -151.63 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1122 0.028 - 0.055: 720 0.055 - 0.083: 224 0.083 - 0.111: 112 0.111 - 0.138: 52 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CA ILE B 136 " pdb=" N ILE B 136 " pdb=" C ILE B 136 " pdb=" CB ILE B 136 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE C 136 " pdb=" N ILE C 136 " pdb=" C ILE C 136 " pdb=" CB ILE C 136 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 136 " pdb=" N ILE A 136 " pdb=" C ILE A 136 " pdb=" CB ILE A 136 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO D 243 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.15e+00 pdb=" N PRO C 243 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO A 243 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.015 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 622 2.72 - 3.26: 15261 3.26 - 3.81: 27311 3.81 - 4.35: 35842 4.35 - 4.90: 56943 Nonbonded interactions: 135979 Sorted by model distance: nonbonded pdb="CA CA D 402 " pdb=" F2 BEF D 403 " model vdw 2.173 2.460 nonbonded pdb="CA CA A 402 " pdb=" F2 BEF A 403 " model vdw 2.173 2.460 nonbonded pdb="CA CA C 402 " pdb=" F2 BEF C 403 " model vdw 2.174 2.460 nonbonded pdb="CA CA E 402 " pdb=" F2 BEF E 403 " model vdw 2.174 2.460 nonbonded pdb="CA CA B 402 " pdb=" F2 BEF B 403 " model vdw 2.174 2.460 ... (remaining 135974 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' } 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: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.070 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.017 0.899 14825 Z= 1.664 Angle : 0.628 13.330 20105 Z= 0.287 Chirality : 0.043 0.138 2230 Planarity : 0.004 0.027 2565 Dihedral : 13.272 151.658 5510 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.65 % Allowed : 3.23 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 1795 helix: -2.30 (0.14), residues: 785 sheet: -0.32 (0.26), residues: 330 loop : 0.94 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 177 TYR 0.008 0.001 TYR B 143 PHE 0.008 0.001 PHE C 262 TRP 0.012 0.002 TRP D 340 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00429 (14820) covalent geometry : angle 0.62766 (20105) hydrogen bonds : bond 0.22397 ( 683) hydrogen bonds : angle 7.93135 ( 1788) Misc. bond : bond 0.89930 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 0.756 Fit side-chains REVERT: C 286 ASP cc_start: 0.7473 (m-30) cc_final: 0.7225 (m-30) REVERT: A 325 MET cc_start: 0.8792 (mmp) cc_final: 0.8531 (mmp) REVERT: B 118 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8311 (tmtt) REVERT: B 227 MET cc_start: 0.9102 (mmm) cc_final: 0.8852 (mmm) REVERT: D 128 ASN cc_start: 0.8190 (m110) cc_final: 0.7964 (m-40) outliers start: 10 outliers final: 0 residues processed: 276 average time/residue: 0.8163 time to fit residues: 242.5342 Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 196 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN A 59 GLN A 225 ASN A 263 GLN A 354 GLN B 246 GLN B 353 GLN D 59 GLN E 353 GLN E 360 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107612 restraints weight = 13993.769| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.10 r_work: 0.3115 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14825 Z= 0.153 Angle : 0.619 8.429 20105 Z= 0.305 Chirality : 0.046 0.178 2230 Planarity : 0.004 0.032 2565 Dihedral : 12.417 166.279 2059 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.45 % Allowed : 8.19 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1795 helix: -0.37 (0.17), residues: 780 sheet: -0.06 (0.26), residues: 330 loop : 1.84 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 95 TYR 0.010 0.001 TYR E 143 PHE 0.011 0.002 PHE D 262 TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00335 (14820) covalent geometry : angle 0.61888 (20105) hydrogen bonds : bond 0.04624 ( 683) hydrogen bonds : angle 5.12382 ( 1788) Misc. bond : bond 0.00124 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.562 Fit side-chains REVERT: C 57 GLU cc_start: 0.8080 (pt0) cc_final: 0.7859 (pt0) REVERT: C 286 ASP cc_start: 0.7875 (m-30) cc_final: 0.7546 (m-30) REVERT: A 118 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.7675 (tmtt) REVERT: B 118 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8394 (tmtt) REVERT: B 176 MET cc_start: 0.8801 (mmt) cc_final: 0.8584 (tpp) REVERT: D 99 GLU cc_start: 0.8350 (pm20) cc_final: 0.8084 (pm20) REVERT: E 82 MET cc_start: 0.8993 (tpt) cc_final: 0.8739 (tpt) REVERT: E 206 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8122 (ttp-110) outliers start: 38 outliers final: 6 residues processed: 233 average time/residue: 0.7105 time to fit residues: 179.4939 Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 53 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 353 GLN A 225 ASN A 263 GLN B 246 GLN B 353 GLN E 40 HIS E 225 ASN E 353 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.103954 restraints weight = 14066.652| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.10 r_work: 0.3050 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 14825 Z= 0.305 Angle : 0.733 9.063 20105 Z= 0.371 Chirality : 0.054 0.210 2230 Planarity : 0.005 0.041 2565 Dihedral : 12.815 176.773 2059 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.06 % Allowed : 8.71 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.20), residues: 1795 helix: 0.09 (0.18), residues: 795 sheet: -0.08 (0.28), residues: 300 loop : 1.64 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 177 TYR 0.011 0.002 TYR E 143 PHE 0.020 0.002 PHE B 262 TRP 0.023 0.004 TRP C 340 HIS 0.009 0.002 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00701 (14820) covalent geometry : angle 0.73257 (20105) hydrogen bonds : bond 0.05885 ( 683) hydrogen bonds : angle 5.16179 ( 1788) Misc. bond : bond 0.00222 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: C 121 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: C 286 ASP cc_start: 0.8066 (m-30) cc_final: 0.7738 (m-30) REVERT: A 72 GLU cc_start: 0.8105 (mp0) cc_final: 0.7508 (mp0) REVERT: A 118 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.7647 (tmtt) REVERT: A 121 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: B 99 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: B 176 MET cc_start: 0.8801 (mmt) cc_final: 0.8583 (tpp) REVERT: B 227 MET cc_start: 0.9140 (mmm) cc_final: 0.8908 (mmm) REVERT: D 99 GLU cc_start: 0.8376 (pm20) cc_final: 0.8036 (pm20) REVERT: D 224 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7558 (mp0) REVERT: E 283 MET cc_start: 0.8688 (mmm) cc_final: 0.8442 (mmp) outliers start: 32 outliers final: 9 residues processed: 218 average time/residue: 0.7435 time to fit residues: 174.8733 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN A 225 ASN A 263 GLN E 225 ASN E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.108495 restraints weight = 14103.834| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.11 r_work: 0.3125 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14825 Z= 0.111 Angle : 0.577 8.135 20105 Z= 0.278 Chirality : 0.044 0.173 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.304 175.679 2059 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.61 % Allowed : 10.06 % Favored : 88.32 % 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: 1.33 (0.20), residues: 1795 helix: 0.65 (0.19), residues: 780 sheet: 0.05 (0.26), residues: 330 loop : 2.02 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.009 0.001 TYR D 69 PHE 0.008 0.001 PHE B 255 TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00238 (14820) covalent geometry : angle 0.57668 (20105) hydrogen bonds : bond 0.03611 ( 683) hydrogen bonds : angle 4.67762 ( 1788) Misc. bond : bond 0.00048 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.585 Fit side-chains REVERT: C 118 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8494 (tttm) REVERT: C 119 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8390 (ttm) REVERT: C 286 ASP cc_start: 0.7905 (m-30) cc_final: 0.7595 (m-30) REVERT: B 99 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: B 118 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8373 (tmtt) REVERT: B 176 MET cc_start: 0.8739 (mmt) cc_final: 0.8504 (tpp) REVERT: B 225 ASN cc_start: 0.8400 (t0) cc_final: 0.7954 (m-40) REVERT: D 224 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7558 (mp0) REVERT: D 226 GLU cc_start: 0.8599 (tp30) cc_final: 0.8271 (tp30) REVERT: D 355 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7631 (mtp) REVERT: E 283 MET cc_start: 0.8569 (mmm) cc_final: 0.8343 (mmp) outliers start: 25 outliers final: 5 residues processed: 220 average time/residue: 0.7596 time to fit residues: 180.8567 Evaluate side-chains 205 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 89 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 263 GLN B 353 GLN E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107706 restraints weight = 14106.184| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.13 r_work: 0.3116 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14825 Z= 0.119 Angle : 0.578 7.853 20105 Z= 0.279 Chirality : 0.044 0.164 2230 Planarity : 0.003 0.032 2565 Dihedral : 12.294 178.448 2059 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.55 % Allowed : 10.77 % Favored : 87.68 % 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: 1.53 (0.20), residues: 1795 helix: 0.85 (0.19), residues: 780 sheet: 0.15 (0.27), residues: 330 loop : 2.07 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 28 TYR 0.008 0.001 TYR D 69 PHE 0.009 0.001 PHE B 255 TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00258 (14820) covalent geometry : angle 0.57800 (20105) hydrogen bonds : bond 0.03714 ( 683) hydrogen bonds : angle 4.59390 ( 1788) Misc. bond : bond 0.00070 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: C 119 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8403 (ttm) REVERT: C 286 ASP cc_start: 0.7912 (m-30) cc_final: 0.7584 (m-30) REVERT: A 326 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8010 (tttt) REVERT: B 64 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8857 (pp) REVERT: B 99 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: B 118 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8410 (tmtt) REVERT: B 176 MET cc_start: 0.8760 (mmt) cc_final: 0.8551 (tpp) REVERT: B 225 ASN cc_start: 0.8387 (t0) cc_final: 0.7928 (m-40) REVERT: B 227 MET cc_start: 0.9113 (mmm) cc_final: 0.8898 (mmm) REVERT: D 224 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7548 (mp0) REVERT: D 226 GLU cc_start: 0.8614 (tp30) cc_final: 0.8386 (tp30) REVERT: D 355 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7633 (mtp) REVERT: E 283 MET cc_start: 0.8556 (mmm) cc_final: 0.8318 (mmp) outliers start: 24 outliers final: 4 residues processed: 217 average time/residue: 0.7705 time to fit residues: 180.8302 Evaluate side-chains 201 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN A 225 ASN A 263 GLN B 353 GLN E 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104959 restraints weight = 13886.934| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.12 r_work: 0.3068 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14825 Z= 0.224 Angle : 0.666 8.582 20105 Z= 0.332 Chirality : 0.049 0.177 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.620 177.373 2059 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.42 % Allowed : 10.77 % Favored : 87.81 % 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: 1.27 (0.20), residues: 1795 helix: 0.67 (0.19), residues: 795 sheet: -0.01 (0.29), residues: 300 loop : 1.83 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 28 TYR 0.009 0.001 TYR E 362 PHE 0.015 0.002 PHE B 262 TRP 0.020 0.003 TRP D 340 HIS 0.007 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00511 (14820) covalent geometry : angle 0.66605 (20105) hydrogen bonds : bond 0.04961 ( 683) hydrogen bonds : angle 4.84469 ( 1788) Misc. bond : bond 0.00175 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: C 119 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8358 (ttm) REVERT: C 286 ASP cc_start: 0.8005 (m-30) cc_final: 0.7667 (m-30) REVERT: A 176 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8082 (mmt) REVERT: B 99 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8220 (pm20) REVERT: B 176 MET cc_start: 0.8773 (mmt) cc_final: 0.8557 (tpp) REVERT: B 225 ASN cc_start: 0.8433 (t0) cc_final: 0.7995 (m-40) REVERT: B 227 MET cc_start: 0.9118 (mmm) cc_final: 0.8876 (mmm) REVERT: D 224 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7582 (mp0) REVERT: D 355 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7632 (mtp) REVERT: E 283 MET cc_start: 0.8613 (mmm) cc_final: 0.8362 (mmp) outliers start: 22 outliers final: 7 residues processed: 207 average time/residue: 0.7850 time to fit residues: 175.2214 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 353 GLN E 225 ASN E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107606 restraints weight = 13954.882| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.10 r_work: 0.3112 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14825 Z= 0.131 Angle : 0.591 8.116 20105 Z= 0.288 Chirality : 0.045 0.175 2230 Planarity : 0.004 0.033 2565 Dihedral : 12.345 177.330 2055 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.55 % Allowed : 10.97 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.55 (0.20), residues: 1795 helix: 0.88 (0.19), residues: 780 sheet: 0.15 (0.27), residues: 330 loop : 2.07 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.008 0.001 TYR D 69 PHE 0.010 0.001 PHE B 262 TRP 0.015 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00288 (14820) covalent geometry : angle 0.59131 (20105) hydrogen bonds : bond 0.03854 ( 683) hydrogen bonds : angle 4.62416 ( 1788) Misc. bond : bond 0.00083 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: C 119 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8372 (ttm) REVERT: C 286 ASP cc_start: 0.7918 (m-30) cc_final: 0.7615 (m-30) REVERT: B 64 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8873 (pp) REVERT: B 99 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: B 176 MET cc_start: 0.8736 (mmt) cc_final: 0.8531 (tpp) REVERT: B 225 ASN cc_start: 0.8380 (t0) cc_final: 0.7945 (m-40) REVERT: D 224 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7530 (mp0) REVERT: D 355 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7617 (mtp) REVERT: E 121 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7760 (tm130) REVERT: E 283 MET cc_start: 0.8544 (mmm) cc_final: 0.8304 (mmp) outliers start: 24 outliers final: 10 residues processed: 210 average time/residue: 0.7467 time to fit residues: 170.0029 Evaluate side-chains 208 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 353 GLN E 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106778 restraints weight = 14091.984| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.10 r_work: 0.3099 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14825 Z= 0.182 Angle : 0.633 8.359 20105 Z= 0.312 Chirality : 0.047 0.175 2230 Planarity : 0.004 0.034 2565 Dihedral : 12.490 177.660 2055 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.48 % Allowed : 11.03 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.49 (0.20), residues: 1795 helix: 0.84 (0.19), residues: 780 sheet: 0.02 (0.29), residues: 300 loop : 2.00 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 28 TYR 0.007 0.001 TYR E 362 PHE 0.013 0.002 PHE B 262 TRP 0.018 0.003 TRP D 340 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00411 (14820) covalent geometry : angle 0.63270 (20105) hydrogen bonds : bond 0.04525 ( 683) hydrogen bonds : angle 4.73848 ( 1788) Misc. bond : bond 0.00124 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: C 119 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8379 (ttm) REVERT: C 286 ASP cc_start: 0.7946 (m-30) cc_final: 0.7616 (m-30) REVERT: B 99 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: B 176 MET cc_start: 0.8743 (mmt) cc_final: 0.8541 (tpp) REVERT: B 225 ASN cc_start: 0.8430 (t0) cc_final: 0.8014 (m-40) REVERT: B 227 MET cc_start: 0.9142 (mmm) cc_final: 0.8839 (mmm) REVERT: D 224 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7583 (mp0) REVERT: D 328 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8347 (tttm) REVERT: D 355 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7668 (mtp) REVERT: E 121 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7820 (tm130) REVERT: E 283 MET cc_start: 0.8595 (mmm) cc_final: 0.8355 (mmp) outliers start: 23 outliers final: 11 residues processed: 205 average time/residue: 0.7726 time to fit residues: 171.2250 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 166 optimal weight: 0.0770 chunk 1 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN E 225 ASN E 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.129125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106982 restraints weight = 14078.254| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.09 r_work: 0.3105 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14825 Z= 0.170 Angle : 0.629 8.341 20105 Z= 0.309 Chirality : 0.047 0.176 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.469 177.523 2055 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.10 % Allowed : 11.48 % Favored : 87.42 % 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: 1.49 (0.20), residues: 1795 helix: 0.84 (0.19), residues: 780 sheet: 0.01 (0.29), residues: 300 loop : 1.99 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 28 TYR 0.007 0.001 TYR E 362 PHE 0.012 0.002 PHE B 262 TRP 0.017 0.003 TRP D 340 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00383 (14820) covalent geometry : angle 0.62874 (20105) hydrogen bonds : bond 0.04351 ( 683) hydrogen bonds : angle 4.70735 ( 1788) Misc. bond : bond 0.00112 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: C 119 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8382 (ttm) REVERT: C 286 ASP cc_start: 0.7935 (m-30) cc_final: 0.7614 (m-30) REVERT: A 225 ASN cc_start: 0.8320 (m-40) cc_final: 0.8025 (m110) REVERT: B 225 ASN cc_start: 0.8422 (t0) cc_final: 0.7998 (m-40) REVERT: B 227 MET cc_start: 0.9141 (mmm) cc_final: 0.8819 (mmm) REVERT: D 224 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7582 (mp0) REVERT: D 226 GLU cc_start: 0.8674 (tp30) cc_final: 0.8471 (tp30) REVERT: D 328 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8337 (tttm) REVERT: D 355 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7662 (mtp) REVERT: E 121 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7832 (tm130) REVERT: E 283 MET cc_start: 0.8581 (mmm) cc_final: 0.8342 (mmp) outliers start: 17 outliers final: 10 residues processed: 200 average time/residue: 0.7394 time to fit residues: 159.8039 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 88 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108384 restraints weight = 14169.691| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.08 r_work: 0.3127 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14825 Z= 0.135 Angle : 0.601 8.027 20105 Z= 0.292 Chirality : 0.045 0.173 2230 Planarity : 0.004 0.047 2565 Dihedral : 12.345 178.457 2055 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.77 % Allowed : 12.06 % Favored : 87.16 % 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: 1.58 (0.20), residues: 1795 helix: 0.91 (0.19), residues: 780 sheet: 0.17 (0.27), residues: 330 loop : 2.07 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 95 TYR 0.008 0.001 TYR D 69 PHE 0.010 0.001 PHE B 262 TRP 0.016 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00299 (14820) covalent geometry : angle 0.60097 (20105) hydrogen bonds : bond 0.03881 ( 683) hydrogen bonds : angle 4.58877 ( 1788) Misc. bond : bond 0.00080 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: C 119 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8398 (ttm) REVERT: C 286 ASP cc_start: 0.7898 (m-30) cc_final: 0.7596 (m-30) REVERT: B 225 ASN cc_start: 0.8408 (t0) cc_final: 0.7979 (m-40) REVERT: B 227 MET cc_start: 0.9138 (mmm) cc_final: 0.8819 (mmm) REVERT: D 224 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7553 (mp0) REVERT: D 226 GLU cc_start: 0.8658 (tp30) cc_final: 0.8454 (tp30) REVERT: D 328 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8321 (tttm) REVERT: D 355 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7645 (mtp) REVERT: E 121 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7822 (tm130) REVERT: E 283 MET cc_start: 0.8533 (mmm) cc_final: 0.8243 (mmp) outliers start: 12 outliers final: 9 residues processed: 204 average time/residue: 0.7307 time to fit residues: 161.1455 Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 121 GLN Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 146 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 225 ASN E 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108936 restraints weight = 13989.604| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.10 r_work: 0.3150 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14825 Z= 0.117 Angle : 0.584 7.781 20105 Z= 0.282 Chirality : 0.044 0.169 2230 Planarity : 0.004 0.045 2565 Dihedral : 12.251 179.675 2055 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.90 % Allowed : 12.19 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.20), residues: 1795 helix: 0.98 (0.19), residues: 780 sheet: 0.21 (0.27), residues: 330 loop : 2.09 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 95 TYR 0.008 0.001 TYR D 69 PHE 0.009 0.001 PHE B 255 TRP 0.015 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00254 (14820) covalent geometry : angle 0.58373 (20105) hydrogen bonds : bond 0.03597 ( 683) hydrogen bonds : angle 4.50176 ( 1788) Misc. bond : bond 0.00063 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6921.48 seconds wall clock time: 118 minutes 24.71 seconds (7104.71 seconds total)