Starting phenix.real_space_refine on Fri Jun 13 16:22:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2u_15107/06_2025/8a2u_15107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2u_15107/06_2025/8a2u_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_15107/06_2025/8a2u_15107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2u_15107/06_2025/8a2u_15107.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2u_15107/06_2025/8a2u_15107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2u_15107/06_2025/8a2u_15107.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.39, per 1000 atoms: 0.69 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: 3.95 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.25 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: 5.98 Time building geometry restraints manager: 4.67 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 39.690 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (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 TRP 0.012 0.002 TRP D 340 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 262 TYR 0.008 0.001 TYR B 143 ARG 0.003 0.001 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.22397 ( 683) hydrogen bonds : angle 7.93135 ( 1788) covalent geometry : bond 0.00429 (14820) covalent geometry : angle 0.62766 (20105) 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 : 2.022 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: 1.6854 time to fit residues: 501.1035 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 : 1.795 ------------------------------------------------------------------------------- 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 151 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 B 246 GLN B 353 GLN D 59 GLN E 353 GLN E 360 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106702 restraints weight = 13986.575| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.10 r_work: 0.3098 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14825 Z= 0.178 Angle : 0.641 8.585 20105 Z= 0.319 Chirality : 0.047 0.182 2230 Planarity : 0.004 0.031 2565 Dihedral : 12.487 169.412 2059 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.65 % Allowed : 8.06 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1795 helix: -0.41 (0.17), residues: 780 sheet: -0.10 (0.26), residues: 330 loop : 1.84 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 340 HIS 0.006 0.001 HIS C 161 PHE 0.014 0.002 PHE D 262 TYR 0.011 0.001 TYR E 143 ARG 0.006 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05030 ( 683) hydrogen bonds : angle 5.14970 ( 1788) covalent geometry : bond 0.00399 (14820) covalent geometry : angle 0.64093 (20105) Misc. bond : bond 0.00185 ( 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 250 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 1.660 Fit side-chains REVERT: C 57 GLU cc_start: 0.8111 (pt0) cc_final: 0.7891 (pt0) REVERT: C 286 ASP cc_start: 0.7913 (m-30) cc_final: 0.7593 (m-30) REVERT: A 118 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.7681 (tmtt) REVERT: B 118 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8380 (tmtt) REVERT: B 176 MET cc_start: 0.8800 (mmt) cc_final: 0.8572 (tpp) REVERT: D 99 GLU cc_start: 0.8361 (pm20) cc_final: 0.8079 (pm20) REVERT: D 224 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7613 (mp0) REVERT: D 271 SER cc_start: 0.8615 (p) cc_final: 0.8399 (t) REVERT: E 82 MET cc_start: 0.9014 (tpt) cc_final: 0.8742 (tpt) outliers start: 41 outliers final: 7 residues processed: 237 average time/residue: 1.5240 time to fit residues: 392.2026 Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 GLU 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 D residue 355 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 291 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 132 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 32 optimal weight: 0.0010 chunk 59 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 59 GLN A 225 ASN A 263 GLN A 354 GLN B 246 GLN B 353 GLN D 59 GLN E 40 HIS E 225 ASN E 353 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107685 restraints weight = 14033.535| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.10 r_work: 0.3114 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14825 Z= 0.129 Angle : 0.587 8.085 20105 Z= 0.285 Chirality : 0.045 0.170 2230 Planarity : 0.004 0.031 2565 Dihedral : 12.307 176.243 2059 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.55 % Allowed : 8.97 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1795 helix: 0.41 (0.18), residues: 780 sheet: 0.01 (0.26), residues: 330 loop : 1.98 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 PHE 0.009 0.001 PHE B 262 TYR 0.007 0.001 TYR E 143 ARG 0.006 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 683) hydrogen bonds : angle 4.79720 ( 1788) covalent geometry : bond 0.00280 (14820) covalent geometry : angle 0.58666 (20105) Misc. bond : bond 0.00082 ( 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 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 1.726 Fit side-chains REVERT: C 118 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8490 (tttm) REVERT: C 119 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8373 (ttm) REVERT: C 286 ASP cc_start: 0.7879 (m-30) cc_final: 0.7549 (m-30) REVERT: A 121 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: B 64 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8860 (pp) REVERT: B 118 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8364 (tmtt) REVERT: B 176 MET cc_start: 0.8730 (mmt) cc_final: 0.8482 (tpp) REVERT: B 227 MET cc_start: 0.9112 (mmm) cc_final: 0.8855 (mmm) REVERT: D 99 GLU cc_start: 0.8333 (pm20) cc_final: 0.8061 (pm20) REVERT: D 224 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7555 (mp0) REVERT: E 283 MET cc_start: 0.8664 (mmm) cc_final: 0.8395 (mmp) outliers start: 24 outliers final: 4 residues processed: 222 average time/residue: 1.5441 time to fit residues: 371.6997 Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain E residue 221 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 143 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 139 optimal weight: 0.5980 chunk 164 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 246 GLN B 353 GLN D 59 GLN E 225 ASN E 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108359 restraints weight = 13978.562| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.10 r_work: 0.3126 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2051 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= 0.120 Angle : 0.575 7.813 20105 Z= 0.278 Chirality : 0.044 0.163 2230 Planarity : 0.003 0.032 2565 Dihedral : 12.269 178.167 2059 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.61 % Allowed : 9.74 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1795 helix: 0.74 (0.19), residues: 780 sheet: 0.10 (0.26), residues: 330 loop : 2.06 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 PHE 0.009 0.001 PHE B 255 TYR 0.007 0.001 TYR A 294 ARG 0.006 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 683) hydrogen bonds : angle 4.62806 ( 1788) covalent geometry : bond 0.00259 (14820) covalent geometry : angle 0.57543 (20105) Misc. bond : bond 0.00064 ( 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 : 1.677 Fit side-chains REVERT: C 118 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8498 (tttm) REVERT: C 119 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8416 (ttm) REVERT: C 286 ASP cc_start: 0.7880 (m-30) cc_final: 0.7541 (m-30) REVERT: A 118 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.7659 (tmtt) REVERT: A 326 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8059 (tttt) REVERT: B 64 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8864 (pp) REVERT: B 118 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8463 (tptm) REVERT: B 176 MET cc_start: 0.8728 (mmt) cc_final: 0.8509 (tpp) REVERT: D 224 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7583 (mp0) REVERT: D 355 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7569 (mtp) REVERT: E 283 MET cc_start: 0.8592 (mmm) cc_final: 0.8335 (mmp) outliers start: 25 outliers final: 2 residues processed: 220 average time/residue: 1.6025 time to fit residues: 381.4621 Evaluate side-chains 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 291 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 60 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 173 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 353 GLN A 225 ASN A 263 GLN B 246 GLN E 225 ASN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103833 restraints weight = 14125.954| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.14 r_work: 0.3048 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14825 Z= 0.224 Angle : 0.666 8.616 20105 Z= 0.331 Chirality : 0.049 0.179 2230 Planarity : 0.004 0.034 2565 Dihedral : 12.618 177.284 2059 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.81 % Allowed : 9.94 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1795 helix: 0.62 (0.19), residues: 795 sheet: -0.03 (0.28), residues: 300 loop : 1.83 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 340 HIS 0.007 0.001 HIS C 161 PHE 0.015 0.002 PHE B 262 TYR 0.009 0.001 TYR E 362 ARG 0.006 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 683) hydrogen bonds : angle 4.86650 ( 1788) covalent geometry : bond 0.00511 (14820) covalent geometry : angle 0.66612 (20105) Misc. bond : bond 0.00162 ( 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 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.685 Fit side-chains REVERT: C 118 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7573 (tmtt) REVERT: C 119 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8371 (ttm) REVERT: C 286 ASP cc_start: 0.8010 (m-30) cc_final: 0.7674 (m-30) REVERT: A 176 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8079 (mmt) REVERT: B 118 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8464 (tptm) REVERT: B 176 MET cc_start: 0.8754 (mmt) cc_final: 0.8531 (tpp) REVERT: B 227 MET cc_start: 0.9115 (mmm) cc_final: 0.8798 (mmm) REVERT: D 224 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7586 (mp0) REVERT: D 355 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7567 (mtp) REVERT: E 283 MET cc_start: 0.8620 (mmm) cc_final: 0.8378 (mmp) outliers start: 28 outliers final: 7 residues processed: 217 average time/residue: 1.6038 time to fit residues: 376.2168 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 118 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 164 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 263 GLN B 246 GLN B 353 GLN E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107826 restraints weight = 14047.141| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.10 r_work: 0.3114 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14825 Z= 0.126 Angle : 0.586 8.121 20105 Z= 0.284 Chirality : 0.045 0.175 2230 Planarity : 0.003 0.033 2565 Dihedral : 12.361 177.183 2059 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.35 % Allowed : 10.65 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1795 helix: 0.86 (0.19), residues: 780 sheet: 0.15 (0.27), residues: 330 loop : 2.06 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 PHE 0.010 0.001 PHE B 262 TYR 0.008 0.001 TYR D 69 ARG 0.006 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 683) hydrogen bonds : angle 4.62634 ( 1788) covalent geometry : bond 0.00276 (14820) covalent geometry : angle 0.58634 (20105) Misc. bond : bond 0.00075 ( 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 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 1.666 Fit side-chains REVERT: C 118 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8490 (tttm) REVERT: C 119 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8389 (ttm) REVERT: C 286 ASP cc_start: 0.7922 (m-30) cc_final: 0.7615 (m-30) REVERT: B 176 MET cc_start: 0.8726 (mmt) cc_final: 0.8515 (tpp) REVERT: D 224 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7586 (mp0) REVERT: D 226 GLU cc_start: 0.8631 (tp30) cc_final: 0.8395 (tp30) REVERT: D 355 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7590 (mtp) REVERT: E 283 MET cc_start: 0.8532 (mmm) cc_final: 0.8250 (mmp) outliers start: 21 outliers final: 5 residues processed: 218 average time/residue: 1.5371 time to fit residues: 363.3382 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 D residue 355 MET Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 355 MET 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 19 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 246 GLN B 353 GLN E 225 ASN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104585 restraints weight = 14136.243| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.08 r_work: 0.3068 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 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 : 0.007 0.055 14825 Z= 0.315 Angle : 0.737 9.009 20105 Z= 0.372 Chirality : 0.054 0.195 2230 Planarity : 0.005 0.046 2565 Dihedral : 12.801 176.573 2055 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.81 % Allowed : 10.06 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1795 helix: 0.53 (0.19), residues: 795 sheet: -0.04 (0.28), residues: 300 loop : 1.74 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP C 340 HIS 0.009 0.002 HIS C 161 PHE 0.020 0.003 PHE B 262 TYR 0.011 0.002 TYR D 166 ARG 0.007 0.001 ARG B 177 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 683) hydrogen bonds : angle 5.00446 ( 1788) covalent geometry : bond 0.00725 (14820) covalent geometry : angle 0.73668 (20105) Misc. bond : bond 0.00246 ( 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 221 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 1.699 Fit side-chains REVERT: C 118 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7636 (tmtt) REVERT: C 119 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8356 (ttm) REVERT: C 121 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8270 (tm-30) REVERT: C 286 ASP cc_start: 0.8050 (m-30) cc_final: 0.7718 (m-30) REVERT: A 176 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8063 (mmt) REVERT: D 224 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7650 (mp0) REVERT: D 355 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7634 (mtp) REVERT: E 283 MET cc_start: 0.8672 (mmm) cc_final: 0.8432 (mmp) outliers start: 28 outliers final: 6 residues processed: 204 average time/residue: 1.5868 time to fit residues: 350.4264 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 192 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 C residue 178 LEU Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 176 MET 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 288 ASP Chi-restraints excluded: chain E residue 291 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 0.6980 chunk 143 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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 225 ASN E 353 GLN E 360 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108928 restraints weight = 14012.273| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.13 r_work: 0.3131 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14825 Z= 0.104 Angle : 0.573 8.033 20105 Z= 0.277 Chirality : 0.044 0.178 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.238 175.444 2055 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.77 % Allowed : 11.48 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.20), residues: 1795 helix: 0.90 (0.19), residues: 780 sheet: 0.14 (0.26), residues: 330 loop : 2.05 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.008 0.001 PHE A 31 TYR 0.009 0.001 TYR A 294 ARG 0.007 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 683) hydrogen bonds : angle 4.55364 ( 1788) covalent geometry : bond 0.00222 (14820) covalent geometry : angle 0.57311 (20105) Misc. bond : bond 0.00035 ( 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 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 1.830 Fit side-chains REVERT: C 118 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8536 (tttm) REVERT: C 119 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8390 (ttm) REVERT: C 286 ASP cc_start: 0.7879 (m-30) cc_final: 0.7587 (m-30) REVERT: D 224 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7517 (mp0) REVERT: D 226 GLU cc_start: 0.8599 (tp30) cc_final: 0.8354 (tp30) REVERT: D 355 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7579 (mtp) REVERT: E 283 MET cc_start: 0.8526 (mmm) cc_final: 0.8239 (mmp) outliers start: 12 outliers final: 6 residues processed: 211 average time/residue: 1.6071 time to fit residues: 367.2909 Evaluate side-chains 207 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 1.753 ------------------------------------------------------------------------------- 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 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 288 ASP Chi-restraints excluded: chain E residue 291 LYS Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 108 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 176 optimal weight: 0.0770 chunk 103 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.129591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.107319 restraints weight = 13921.067| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.09 r_work: 0.3108 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14825 Z= 0.169 Angle : 0.624 8.270 20105 Z= 0.307 Chirality : 0.047 0.172 2230 Planarity : 0.004 0.034 2565 Dihedral : 12.438 177.416 2055 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.97 % Allowed : 11.48 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.20), residues: 1795 helix: 0.86 (0.19), residues: 780 sheet: 0.16 (0.27), residues: 330 loop : 2.06 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 340 HIS 0.006 0.001 HIS C 161 PHE 0.012 0.002 PHE B 262 TYR 0.008 0.001 TYR E 362 ARG 0.007 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 683) hydrogen bonds : angle 4.68108 ( 1788) covalent geometry : bond 0.00377 (14820) covalent geometry : angle 0.62401 (20105) Misc. bond : bond 0.00123 ( 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 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 2.089 Fit side-chains REVERT: C 118 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8411 (tttp) REVERT: C 119 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8399 (ttm) REVERT: C 286 ASP cc_start: 0.7956 (m-30) cc_final: 0.7609 (m-30) REVERT: B 222 ASP cc_start: 0.8543 (t70) cc_final: 0.8332 (t0) REVERT: B 227 MET cc_start: 0.9125 (mmm) cc_final: 0.8883 (mmm) REVERT: D 224 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7580 (mp0) REVERT: D 226 GLU cc_start: 0.8621 (tp30) cc_final: 0.8343 (tp30) REVERT: D 355 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7604 (mtp) REVERT: E 283 MET cc_start: 0.8580 (mmm) cc_final: 0.8288 (mmp) outliers start: 15 outliers final: 5 residues processed: 205 average time/residue: 1.9022 time to fit residues: 423.3385 Evaluate side-chains 209 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 201 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 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 288 ASP Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 76 optimal weight: 0.4980 chunk 45 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 E 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110446 restraints weight = 14108.754| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.09 r_work: 0.3158 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14825 Z= 0.101 Angle : 0.569 7.632 20105 Z= 0.273 Chirality : 0.044 0.170 2230 Planarity : 0.003 0.042 2565 Dihedral : 12.189 178.349 2055 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.58 % Allowed : 11.68 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.20), residues: 1795 helix: 0.98 (0.19), residues: 780 sheet: 0.21 (0.27), residues: 330 loop : 2.07 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.008 0.001 PHE B 31 TYR 0.008 0.001 TYR D 69 ARG 0.009 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 683) hydrogen bonds : angle 4.46188 ( 1788) covalent geometry : bond 0.00215 (14820) covalent geometry : angle 0.56909 (20105) Misc. bond : bond 0.00026 ( 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 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 2.476 Fit side-chains REVERT: C 118 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8518 (tttm) REVERT: B 227 MET cc_start: 0.9120 (mmm) cc_final: 0.8864 (mmm) REVERT: D 224 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7538 (mp0) REVERT: D 355 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7652 (mtp) REVERT: E 283 MET cc_start: 0.8490 (mmm) cc_final: 0.8224 (mmp) outliers start: 9 outliers final: 2 residues processed: 208 average time/residue: 1.6903 time to fit residues: 380.6519 Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 198 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 65 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 E 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105326 restraints weight = 14024.596| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.10 r_work: 0.3074 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14825 Z= 0.278 Angle : 0.720 8.878 20105 Z= 0.361 Chirality : 0.052 0.188 2230 Planarity : 0.005 0.052 2565 Dihedral : 12.726 176.781 2055 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.58 % Allowed : 11.81 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1795 helix: 0.63 (0.19), residues: 795 sheet: -0.01 (0.28), residues: 300 loop : 1.79 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP D 340 HIS 0.008 0.002 HIS C 161 PHE 0.018 0.002 PHE B 262 TYR 0.009 0.002 TYR D 166 ARG 0.009 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.05457 ( 683) hydrogen bonds : angle 4.90821 ( 1788) covalent geometry : bond 0.00637 (14820) covalent geometry : angle 0.72046 (20105) Misc. bond : bond 0.00227 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14433.22 seconds wall clock time: 251 minutes 24.40 seconds (15084.40 seconds total)