Starting phenix.real_space_refine on Fri Jul 3 19:33:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ad9_11721/07_2026/7ad9_11721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ad9_11721/07_2026/7ad9_11721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ad9_11721/07_2026/7ad9_11721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ad9_11721/07_2026/7ad9_11721.map" model { file = "/net/cci-nas-00/data/ceres_data/7ad9_11721/07_2026/7ad9_11721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ad9_11721/07_2026/7ad9_11721.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ad9_11721/07_2026/7ad9_11721.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ad9_11721/07_2026/7ad9_11721.cif" } resolution = 3.5 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= 0.002 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 9810 2.51 5 N 2605 2.21 5 O 3010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15560 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "L" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "H" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "I" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "Q" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.83, per 1000 atoms: 0.18 Number of scatterers: 15560 At special positions: 0 Unit cell: (99.22, 91.96, 191.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 15 15.00 Mg 5 11.99 O 3010 8.00 N 2605 7.00 C 9810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied TRANS " DTH O 6 " - " ALA O 5 " " DTH P 6 " - " ALA P 5 " " DTH Q 6 " - " ALA Q 5 " " DTH R 6 " - " ALA R 5 " " DTH S 6 " - " ALA S 5 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 450.0 milliseconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH O 6 " pdb=" CB DTH P 6 " pdb=" CB DTH Q 6 " pdb=" CB DTH R 6 " pdb=" CB DTH S 6 " Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 30 sheets defined 54.2% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.078A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.775A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 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 257 Processing helix chain 'B' and resid 258 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: 3.613A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.536A pdb=" N ARG B 335 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 332 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.222A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.531A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 2 through 16 Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.077A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.774A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 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 257 Processing helix chain 'D' and resid 258 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: 3.613A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.536A pdb=" N ARG D 335 " --> pdb=" O PRO D 332 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS D 336 " --> pdb=" O PRO D 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 332 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 353 removed outlier: 6.223A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.531A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'H' and resid 44 through 48 Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.077A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 removed outlier: 3.775A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 288 No H-bonds generated for 'chain 'H' and resid 286 through 288' Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 301 through 306 removed outlier: 3.612A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 318 Processing helix chain 'H' and resid 332 through 336 removed outlier: 3.536A pdb=" N ARG H 335 " --> pdb=" O PRO H 332 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS H 336 " --> pdb=" O PRO H 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 332 through 336' Processing helix chain 'H' and resid 337 through 347 Processing helix chain 'H' and resid 348 through 353 removed outlier: 6.223A pdb=" N THR H 351 " --> pdb=" O SER H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 removed outlier: 3.530A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 372 Processing helix chain 'E' and resid 2 through 16 Processing helix chain 'F' and resid 44 through 48 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 61 through 65 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.078A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 removed outlier: 3.775A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.613A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 318 Processing helix chain 'F' and resid 332 through 336 removed outlier: 3.537A pdb=" N ARG F 335 " --> pdb=" O PRO F 332 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS F 336 " --> pdb=" O PRO F 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 332 through 336' Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'F' and resid 348 through 353 removed outlier: 6.222A pdb=" N THR F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 removed outlier: 3.531A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 372 Processing helix chain 'G' and resid 2 through 16 Processing helix chain 'I' and resid 44 through 48 Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 112 through 126 removed outlier: 4.078A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 removed outlier: 3.775A pdb=" N LEU I 142 " --> pdb=" O ALA I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 194 through 197 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 258 through 262 Processing helix chain 'I' and resid 263 through 268 Processing helix chain 'I' and resid 273 through 284 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 289 through 295 Processing helix chain 'I' and resid 301 through 306 removed outlier: 3.612A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 318 Processing helix chain 'I' and resid 332 through 336 removed outlier: 3.536A pdb=" N ARG I 335 " --> pdb=" O PRO I 332 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS I 336 " --> pdb=" O PRO I 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 332 through 336' Processing helix chain 'I' and resid 337 through 347 Processing helix chain 'I' and resid 348 through 353 removed outlier: 6.223A pdb=" N THR I 351 " --> pdb=" O SER I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 removed outlier: 3.531A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 21 removed outlier: 6.661A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.467A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 21 removed outlier: 6.660A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.468A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 21 removed outlier: 6.660A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.469A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'F' and resid 17 through 21 removed outlier: 6.660A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AC3, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.468A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'I' and resid 17 through 21 removed outlier: 6.661A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA I 135 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.468A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 238 through 241 730 hydrogen bonds defined for protein. 1755 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: 2.34 Time building geometry restraints manager: 1.42 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: 4914 1.34 - 1.46: 3552 1.46 - 1.58: 7199 1.58 - 1.70: 15 1.70 - 1.82: 200 Bond restraints: 15880 Sorted by residual: bond pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.49e+01 bond pdb=" CA ILE F 151 " pdb=" C ILE F 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.46e+01 bond pdb=" CA ILE H 151 " pdb=" C ILE H 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.45e+01 bond pdb=" CA ILE I 151 " pdb=" C ILE I 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.44e+01 bond pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 1.522 1.464 0.058 1.19e-02 7.06e+03 2.41e+01 ... (remaining 15875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18223 2.03 - 4.05: 2671 4.05 - 6.08: 492 6.08 - 8.10: 106 8.10 - 10.13: 38 Bond angle restraints: 21530 Sorted by residual: angle pdb=" N VAL F 54 " pdb=" CA VAL F 54 " pdb=" C VAL F 54 " ideal model delta sigma weight residual 108.12 115.88 -7.76 1.44e+00 4.82e-01 2.91e+01 angle pdb=" N VAL B 54 " pdb=" CA VAL B 54 " pdb=" C VAL B 54 " ideal model delta sigma weight residual 108.12 115.86 -7.74 1.44e+00 4.82e-01 2.89e+01 angle pdb=" N VAL I 54 " pdb=" CA VAL I 54 " pdb=" C VAL I 54 " ideal model delta sigma weight residual 108.12 115.85 -7.73 1.44e+00 4.82e-01 2.88e+01 angle pdb=" N VAL D 54 " pdb=" CA VAL D 54 " pdb=" C VAL D 54 " ideal model delta sigma weight residual 108.12 115.84 -7.72 1.44e+00 4.82e-01 2.87e+01 angle pdb=" N VAL H 54 " pdb=" CA VAL H 54 " pdb=" C VAL H 54 " ideal model delta sigma weight residual 108.12 115.84 -7.72 1.44e+00 4.82e-01 2.87e+01 ... (remaining 21525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.01: 9325 29.01 - 58.02: 155 58.02 - 87.02: 20 87.02 - 116.03: 5 116.03 - 145.04: 10 Dihedral angle restraints: 9515 sinusoidal: 3840 harmonic: 5675 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.04 -145.04 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.02 -145.02 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PB ADP H 401 " pdb=" PA ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.01 -145.01 1 2.00e+01 2.50e-03 4.37e+01 ... (remaining 9512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 2390 1.007 - 2.014: 0 2.014 - 3.022: 0 3.022 - 4.029: 0 4.029 - 5.036: 10 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CA DTH O 6 " pdb=" N DTH O 6 " pdb=" C DTH O 6 " pdb=" CB DTH O 6 " both_signs ideal model delta sigma weight residual False 2.53 -2.51 5.04 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" CA DTH P 6 " pdb=" N DTH P 6 " pdb=" C DTH P 6 " pdb=" CB DTH P 6 " both_signs ideal model delta sigma weight residual False 2.53 -2.51 5.04 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" CA DTH R 6 " pdb=" N DTH R 6 " pdb=" C DTH R 6 " pdb=" CB DTH R 6 " both_signs ideal model delta sigma weight residual False 2.53 -2.51 5.04 2.00e-01 2.50e+01 6.34e+02 ... (remaining 2397 not shown) Planarity restraints: 2725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 11 " -0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" CG ASP D 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP D 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP D 11 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 11 " -0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" CG ASP I 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP I 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP I 11 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 11 " -0.028 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" CG ASP H 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP H 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP H 11 " -0.034 2.00e-02 2.50e+03 ... (remaining 2722 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 30 2.39 - 3.02: 9825 3.02 - 3.65: 23068 3.65 - 4.27: 38920 4.27 - 4.90: 61432 Nonbonded interactions: 133275 Sorted by model distance: nonbonded pdb=" CD1 TRP R 3 " pdb=" SG CYS R 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP P 3 " pdb=" SG CYS P 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP S 3 " pdb=" SG CYS S 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP O 3 " pdb=" SG CYS O 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP Q 3 " pdb=" SG CYS Q 7 " model vdw 1.766 3.620 ... (remaining 133270 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'L' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.370 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 0.093 15890 Z= 0.843 Angle : 1.608 10.129 21545 Z= 0.979 Chirality : 0.335 5.036 2400 Planarity : 0.011 0.057 2720 Dihedral : 12.373 145.040 5860 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.39 % Cbeta Deviations : 0.27 % 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: -0.26 (0.19), residues: 1900 helix: -1.30 (0.15), residues: 880 sheet: 0.22 (0.33), residues: 225 loop : 1.47 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.004 ARG I 116 TYR 0.063 0.007 TYR B 143 PHE 0.053 0.008 PHE B 124 TRP 0.031 0.005 TRP H 340 HIS 0.031 0.007 HIS F 40 Details of bonding type rmsd/Z covalent geometry : bond 0.01667 / 0.83 (15880) covalent geometry : angle 1.60651 / 0.98 (21530) hydrogen bonds : bond 0.13841 / 9.05 ( 720) hydrogen bonds : angle 6.76617 / 4.72 ( 1755) Misc. bond : bond 0.07779 / 4.54 ( 5) link_TRANS : bond 0.03526 / 2.06 ( 5) link_TRANS : angle 3.02162 / 1.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 438 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ASN cc_start: 0.7662 (t0) cc_final: 0.6847 (t0) REVERT: B 82 MET cc_start: 0.9072 (tpt) cc_final: 0.8852 (tpt) REVERT: B 190 MET cc_start: 0.7943 (mtp) cc_final: 0.7630 (mtp) REVERT: B 305 MET cc_start: 0.8823 (mmm) cc_final: 0.8482 (mmt) REVERT: B 326 LYS cc_start: 0.8131 (tptt) cc_final: 0.7749 (tttt) REVERT: D 113 LYS cc_start: 0.7920 (mttt) cc_final: 0.7673 (mtmt) REVERT: D 115 ASN cc_start: 0.8415 (t0) cc_final: 0.8187 (t0) REVERT: D 119 MET cc_start: 0.8350 (ttp) cc_final: 0.8139 (ttm) REVERT: D 151 ILE cc_start: 0.8854 (mt) cc_final: 0.8583 (mt) REVERT: H 44 MET cc_start: 0.7546 (mtp) cc_final: 0.7341 (mtm) REVERT: H 115 ASN cc_start: 0.8445 (t0) cc_final: 0.8081 (m-40) REVERT: F 305 MET cc_start: 0.8620 (mmm) cc_final: 0.8213 (mmt) REVERT: I 154 ASP cc_start: 0.8289 (t0) cc_final: 0.7895 (t70) REVERT: I 225 ASN cc_start: 0.8339 (m-40) cc_final: 0.7865 (m110) REVERT: I 274 ILE cc_start: 0.8022 (pt) cc_final: 0.7808 (tt) REVERT: I 283 MET cc_start: 0.8566 (mmp) cc_final: 0.8354 (mmt) outliers start: 5 outliers final: 0 residues processed: 441 average time/residue: 0.1162 time to fit residues: 74.4091 Evaluate side-chains 202 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN D 40 HIS D 246 GLN H 40 HIS H 59 GLN H 121 GLN H 353 GLN F 12 ASN F 49 GLN F 121 GLN I 128 ASN I 314 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089145 restraints weight = 31053.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091745 restraints weight = 15283.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.093442 restraints weight = 9054.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.094559 restraints weight = 6111.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.095307 restraints weight = 4549.840| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15890 Z= 0.158 Angle : 0.677 8.019 21545 Z= 0.340 Chirality : 0.049 0.367 2400 Planarity : 0.004 0.049 2720 Dihedral : 10.469 115.954 2195 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.55 % Allowed : 7.54 % Favored : 89.91 % Cbeta Deviations : 0.27 % 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: 0.89 (0.19), residues: 1900 helix: 0.27 (0.17), residues: 840 sheet: 0.35 (0.34), residues: 235 loop : 1.34 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 147 TYR 0.017 0.001 TYR H 294 PHE 0.034 0.002 PHE D 375 TRP 0.018 0.002 TRP I 340 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (15880) covalent geometry : angle 0.66885 / 0.33 (21530) hydrogen bonds : bond 0.03656 / 2.41 ( 720) hydrogen bonds : angle 4.59539 / 3.20 ( 1755) Misc. bond : bond 0.00188 / 0.12 ( 5) link_TRANS : bond 0.00773 / 0.45 ( 5) link_TRANS : angle 4.02545 / 2.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.7327 (mmm) cc_final: 0.6985 (mmm) REVERT: B 325 MET cc_start: 0.6563 (mtm) cc_final: 0.6226 (mtt) REVERT: B 326 LYS cc_start: 0.8054 (tptt) cc_final: 0.7839 (tttt) REVERT: D 119 MET cc_start: 0.8277 (ttp) cc_final: 0.8035 (ttm) REVERT: L 11 GLU cc_start: 0.7668 (tp30) cc_final: 0.7445 (tp30) REVERT: H 115 ASN cc_start: 0.8236 (t0) cc_final: 0.7870 (m-40) REVERT: H 128 ASN cc_start: 0.7817 (m-40) cc_final: 0.7409 (t0) REVERT: H 206 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.6781 (ttp80) REVERT: H 305 MET cc_start: 0.8702 (mmm) cc_final: 0.8499 (mmm) REVERT: F 157 ASP cc_start: 0.7973 (t70) cc_final: 0.7681 (t0) REVERT: F 176 MET cc_start: 0.7973 (mmm) cc_final: 0.7752 (mmt) REVERT: F 337 TYR cc_start: 0.7512 (m-80) cc_final: 0.7228 (m-80) REVERT: F 344 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8698 (m) REVERT: G 1 MET cc_start: 0.6032 (ptt) cc_final: 0.4888 (ptm) REVERT: G 9 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7205 (ttpp) REVERT: I 12 ASN cc_start: 0.7326 (m110) cc_final: 0.6772 (p0) REVERT: I 95 ARG cc_start: 0.7643 (mmm160) cc_final: 0.6973 (mmt180) REVERT: I 154 ASP cc_start: 0.8205 (t0) cc_final: 0.7790 (t70) REVERT: I 178 LEU cc_start: 0.8738 (mt) cc_final: 0.8530 (mt) REVERT: I 225 ASN cc_start: 0.8317 (m-40) cc_final: 0.7692 (m110) REVERT: I 289 ILE cc_start: 0.8489 (mm) cc_final: 0.8220 (mm) outliers start: 42 outliers final: 16 residues processed: 277 average time/residue: 0.1046 time to fit residues: 44.0599 Evaluate side-chains 207 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain I residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 145 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS H 297 ASN F 115 ASN I 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.082942 restraints weight = 31196.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.085482 restraints weight = 15597.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087139 restraints weight = 9381.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088249 restraints weight = 6433.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.088912 restraints weight = 4844.577| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 15890 Z= 0.172 Angle : 0.634 7.477 21545 Z= 0.311 Chirality : 0.048 0.284 2400 Planarity : 0.004 0.060 2720 Dihedral : 9.316 107.144 2195 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.61 % Allowed : 9.85 % Favored : 87.54 % Cbeta Deviations : 0.27 % 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: 1.04 (0.19), residues: 1900 helix: 0.53 (0.18), residues: 840 sheet: 0.40 (0.35), residues: 225 loop : 1.25 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.015 0.002 TYR H 53 PHE 0.021 0.002 PHE D 375 TRP 0.017 0.002 TRP D 340 HIS 0.004 0.001 HIS F 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (15880) covalent geometry : angle 0.63260 / 0.31 (21530) hydrogen bonds : bond 0.03453 / 2.31 ( 720) hydrogen bonds : angle 4.61750 / 3.19 ( 1755) Misc. bond : bond 0.00047 / 0.03 ( 5) link_TRANS : bond 0.00494 / 0.25 ( 5) link_TRANS : angle 1.94385 / 1.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9007 (tt) REVERT: B 205 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 325 MET cc_start: 0.6600 (mtm) cc_final: 0.6371 (mtt) REVERT: D 119 MET cc_start: 0.8250 (ttp) cc_final: 0.7994 (ttm) REVERT: D 132 MET cc_start: 0.7958 (tmm) cc_final: 0.7708 (tmm) REVERT: D 352 PHE cc_start: 0.9088 (t80) cc_final: 0.8865 (t80) REVERT: H 47 MET cc_start: 0.5942 (ttp) cc_final: 0.4708 (tmm) REVERT: H 352 PHE cc_start: 0.8873 (t80) cc_final: 0.8621 (t80) REVERT: E 6 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8046 (mt) REVERT: E 8 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7713 (mtmt) REVERT: F 176 MET cc_start: 0.8121 (mmm) cc_final: 0.7835 (mmt) REVERT: F 344 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.8726 (m) REVERT: G 9 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7391 (ttpp) REVERT: I 12 ASN cc_start: 0.7389 (m110) cc_final: 0.6886 (p0) REVERT: I 78 ASN cc_start: 0.6324 (t0) cc_final: 0.5361 (t0) REVERT: I 81 ASP cc_start: 0.7391 (m-30) cc_final: 0.7081 (m-30) REVERT: I 132 MET cc_start: 0.8018 (ptp) cc_final: 0.7713 (ptp) REVERT: I 141 SER cc_start: 0.8889 (m) cc_final: 0.8658 (m) REVERT: I 154 ASP cc_start: 0.8248 (t0) cc_final: 0.7866 (t70) REVERT: I 289 ILE cc_start: 0.8611 (mm) cc_final: 0.8332 (mm) outliers start: 43 outliers final: 25 residues processed: 235 average time/residue: 0.1063 time to fit residues: 38.6365 Evaluate side-chains 212 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 142 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 155 optimal weight: 0.0070 chunk 166 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 134 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 297 ASN I 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.095850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085035 restraints weight = 31123.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.087544 restraints weight = 15397.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.089173 restraints weight = 9272.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.090294 restraints weight = 6387.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.091077 restraints weight = 4798.676| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15890 Z= 0.104 Angle : 0.562 7.864 21545 Z= 0.270 Chirality : 0.045 0.200 2400 Planarity : 0.004 0.056 2720 Dihedral : 8.294 95.304 2195 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.01 % Allowed : 11.12 % Favored : 86.87 % Cbeta Deviations : 0.27 % 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: 1900 helix: 0.82 (0.19), residues: 840 sheet: 0.27 (0.34), residues: 235 loop : 1.35 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 335 TYR 0.010 0.001 TYR I 294 PHE 0.018 0.001 PHE H 375 TRP 0.013 0.001 TRP D 340 HIS 0.003 0.001 HIS I 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (15880) covalent geometry : angle 0.56110 / 0.27 (21530) hydrogen bonds : bond 0.02744 / 1.81 ( 720) hydrogen bonds : angle 4.37380 / 3.01 ( 1755) Misc. bond : bond 0.00044 / 0.03 ( 5) link_TRANS : bond 0.00163 / 0.08 ( 5) link_TRANS : angle 1.11738 / 0.59 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 205 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7224 (mt-10) REVERT: D 119 MET cc_start: 0.8096 (ttp) cc_final: 0.7889 (ttm) REVERT: H 47 MET cc_start: 0.5905 (ttp) cc_final: 0.4625 (tmm) REVERT: E 6 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8195 (mt) REVERT: E 8 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7789 (mtmt) REVERT: F 344 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.8976 (m) REVERT: G 9 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7342 (ttmm) REVERT: I 12 ASN cc_start: 0.7221 (m110) cc_final: 0.6771 (p0) REVERT: I 141 SER cc_start: 0.8871 (m) cc_final: 0.8601 (m) REVERT: I 154 ASP cc_start: 0.8318 (t0) cc_final: 0.7965 (t70) REVERT: I 289 ILE cc_start: 0.8510 (mm) cc_final: 0.8170 (mm) outliers start: 33 outliers final: 13 residues processed: 225 average time/residue: 0.1097 time to fit residues: 38.5412 Evaluate side-chains 195 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 115 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 184 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.0050 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN B 101 HIS D 246 GLN H 297 ASN I 78 ASN I 115 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.093048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.082249 restraints weight = 31342.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084713 restraints weight = 15589.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086342 restraints weight = 9397.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087420 restraints weight = 6464.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088176 restraints weight = 4886.094| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15890 Z= 0.142 Angle : 0.588 9.124 21545 Z= 0.281 Chirality : 0.046 0.202 2400 Planarity : 0.004 0.060 2720 Dihedral : 7.373 76.310 2195 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.13 % Allowed : 12.40 % Favored : 85.47 % Cbeta Deviations : 0.27 % 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: 1900 helix: 0.84 (0.19), residues: 845 sheet: 0.33 (0.36), residues: 225 loop : 1.28 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 335 TYR 0.012 0.001 TYR H 143 PHE 0.018 0.002 PHE H 375 TRP 0.016 0.001 TRP D 340 HIS 0.003 0.001 HIS F 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (15880) covalent geometry : angle 0.58718 / 0.28 (21530) hydrogen bonds : bond 0.02968 / 1.95 ( 720) hydrogen bonds : angle 4.41014 / 3.04 ( 1755) Misc. bond : bond 0.00019 / 0.01 ( 5) link_TRANS : bond 0.00074 / 0.04 ( 5) link_TRANS : angle 1.19381 / 0.66 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: B 205 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7208 (mt-10) REVERT: D 119 MET cc_start: 0.8129 (ttp) cc_final: 0.7909 (ttm) REVERT: D 133 TYR cc_start: 0.8651 (t80) cc_final: 0.8338 (t80) REVERT: D 248 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8547 (pt) REVERT: H 47 MET cc_start: 0.6122 (ttp) cc_final: 0.4782 (tmm) REVERT: H 305 MET cc_start: 0.8504 (mmm) cc_final: 0.8270 (mtt) REVERT: H 355 MET cc_start: 0.7771 (mtp) cc_final: 0.7352 (mtt) REVERT: E 6 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8288 (mt) REVERT: E 8 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7777 (mtmt) REVERT: F 198 TYR cc_start: 0.8572 (m-80) cc_final: 0.8290 (m-80) REVERT: F 313 MET cc_start: 0.8778 (tpp) cc_final: 0.8545 (ttm) REVERT: G 9 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7457 (ttmm) REVERT: I 12 ASN cc_start: 0.7470 (m110) cc_final: 0.7003 (p0) REVERT: I 154 ASP cc_start: 0.8320 (t0) cc_final: 0.7974 (t70) REVERT: I 289 ILE cc_start: 0.8582 (mm) cc_final: 0.8241 (mm) outliers start: 35 outliers final: 21 residues processed: 204 average time/residue: 0.1061 time to fit residues: 34.5147 Evaluate side-chains 196 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 297 ASN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 182 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.090938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080118 restraints weight = 31260.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.082482 restraints weight = 15714.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.084100 restraints weight = 9627.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.085145 restraints weight = 6659.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085895 restraints weight = 5085.935| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15890 Z= 0.194 Angle : 0.616 7.450 21545 Z= 0.298 Chirality : 0.048 0.220 2400 Planarity : 0.004 0.059 2720 Dihedral : 7.064 70.980 2195 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.31 % Allowed : 12.46 % Favored : 85.23 % Cbeta Deviations : 0.27 % 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: 1.04 (0.20), residues: 1900 helix: 0.73 (0.19), residues: 845 sheet: 0.08 (0.34), residues: 225 loop : 1.11 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 335 TYR 0.016 0.001 TYR H 143 PHE 0.050 0.002 PHE H 352 TRP 0.017 0.002 TRP D 340 HIS 0.004 0.001 HIS F 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (15880) covalent geometry : angle 0.61509 / 0.30 (21530) hydrogen bonds : bond 0.03152 / 2.09 ( 720) hydrogen bonds : angle 4.54333 / 3.13 ( 1755) Misc. bond : bond 0.00023 / 0.02 ( 5) link_TRANS : bond 0.00172 / 0.10 ( 5) link_TRANS : angle 1.28318 / 0.74 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5728 (ptt) cc_final: 0.4616 (mtm) REVERT: B 205 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7089 (mt-10) REVERT: D 119 MET cc_start: 0.8097 (ttp) cc_final: 0.7867 (ttm) REVERT: D 248 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8586 (pt) REVERT: H 47 MET cc_start: 0.6219 (ttp) cc_final: 0.4771 (tmm) REVERT: H 305 MET cc_start: 0.8517 (mmm) cc_final: 0.8233 (mtt) REVERT: H 355 MET cc_start: 0.7759 (mtp) cc_final: 0.7529 (mtt) REVERT: E 6 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8306 (mt) REVERT: E 8 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7766 (mtmt) REVERT: F 176 MET cc_start: 0.8055 (mmm) cc_final: 0.7769 (mmt) REVERT: F 313 MET cc_start: 0.8783 (tpp) cc_final: 0.8532 (ttm) REVERT: G 9 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7431 (ttmm) REVERT: I 12 ASN cc_start: 0.7682 (m110) cc_final: 0.7263 (p0) REVERT: I 154 ASP cc_start: 0.8280 (t0) cc_final: 0.8038 (t70) REVERT: I 289 ILE cc_start: 0.8564 (mm) cc_final: 0.8297 (mm) REVERT: I 300 SER cc_start: 0.8190 (p) cc_final: 0.7904 (m) outliers start: 38 outliers final: 28 residues processed: 198 average time/residue: 0.0966 time to fit residues: 30.7280 Evaluate side-chains 195 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 297 ASN Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 357 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 55 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 163 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN H 12 ASN F 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.083005 restraints weight = 30837.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085477 restraints weight = 15372.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.087079 restraints weight = 9271.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088169 restraints weight = 6422.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088873 restraints weight = 4860.029| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15890 Z= 0.103 Angle : 0.551 7.030 21545 Z= 0.263 Chirality : 0.045 0.214 2400 Planarity : 0.004 0.056 2720 Dihedral : 6.732 72.872 2195 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.70 % Allowed : 13.07 % Favored : 85.23 % Cbeta Deviations : 0.27 % 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: 1.22 (0.20), residues: 1900 helix: 0.92 (0.19), residues: 845 sheet: 0.11 (0.35), residues: 225 loop : 1.17 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 335 TYR 0.015 0.001 TYR F 133 PHE 0.040 0.001 PHE H 352 TRP 0.015 0.001 TRP D 340 HIS 0.003 0.001 HIS I 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 (15880) covalent geometry : angle 0.55056 / 0.26 (21530) hydrogen bonds : bond 0.02633 / 1.74 ( 720) hydrogen bonds : angle 4.35581 / 2.99 ( 1755) Misc. bond : bond 0.00047 / 0.04 ( 5) link_TRANS : bond 0.00124 / 0.06 ( 5) link_TRANS : angle 1.20275 / 0.64 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5540 (ptt) cc_final: 0.4619 (mtm) REVERT: B 205 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7177 (mt-10) REVERT: H 47 MET cc_start: 0.6198 (ttp) cc_final: 0.4924 (tmm) REVERT: E 6 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8289 (mt) REVERT: E 8 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7778 (mtmt) REVERT: G 9 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7530 (ttmm) REVERT: I 12 ASN cc_start: 0.7694 (m110) cc_final: 0.7226 (p0) REVERT: I 154 ASP cc_start: 0.8165 (t0) cc_final: 0.7822 (t70) REVERT: I 289 ILE cc_start: 0.8315 (mm) cc_final: 0.8015 (mm) outliers start: 28 outliers final: 20 residues processed: 204 average time/residue: 0.1044 time to fit residues: 34.2741 Evaluate side-chains 193 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 81 optimal weight: 0.0020 chunk 61 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 0.0770 chunk 76 optimal weight: 10.0000 overall best weight: 0.7748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN I 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.082853 restraints weight = 31192.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.085259 restraints weight = 15492.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.086911 restraints weight = 9427.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088002 restraints weight = 6469.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.088755 restraints weight = 4892.141| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15890 Z= 0.110 Angle : 0.560 8.396 21545 Z= 0.267 Chirality : 0.045 0.202 2400 Planarity : 0.004 0.056 2720 Dihedral : 6.638 74.376 2195 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.82 % Allowed : 13.62 % Favored : 84.56 % Cbeta Deviations : 0.27 % 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: 1.20 (0.20), residues: 1900 helix: 0.92 (0.19), residues: 845 sheet: 0.07 (0.35), residues: 225 loop : 1.15 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 335 TYR 0.011 0.001 TYR F 133 PHE 0.037 0.001 PHE H 352 TRP 0.016 0.001 TRP D 340 HIS 0.003 0.001 HIS F 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (15880) covalent geometry : angle 0.55897 / 0.27 (21530) hydrogen bonds : bond 0.02653 / 1.76 ( 720) hydrogen bonds : angle 4.31260 / 2.95 ( 1755) Misc. bond : bond 0.00041 / 0.03 ( 5) link_TRANS : bond 0.00116 / 0.06 ( 5) link_TRANS : angle 1.21034 / 0.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5495 (ptt) cc_final: 0.4633 (mtm) REVERT: B 205 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7201 (mt-10) REVERT: C 1 MET cc_start: 0.4220 (ppp) cc_final: 0.4000 (ppp) REVERT: H 44 MET cc_start: 0.7207 (mtm) cc_final: 0.6906 (mtm) REVERT: H 47 MET cc_start: 0.6219 (ttp) cc_final: 0.4833 (tmm) REVERT: E 8 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7803 (mtmt) REVERT: G 9 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7581 (ttmm) REVERT: I 12 ASN cc_start: 0.7702 (m110) cc_final: 0.7227 (p0) REVERT: I 132 MET cc_start: 0.8678 (pmm) cc_final: 0.8230 (pmm) REVERT: I 137 GLN cc_start: 0.8432 (mp10) cc_final: 0.8227 (mt0) REVERT: I 289 ILE cc_start: 0.8335 (mm) cc_final: 0.8063 (mm) outliers start: 30 outliers final: 21 residues processed: 207 average time/residue: 0.1043 time to fit residues: 34.4933 Evaluate side-chains 186 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 115 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN I 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.082263 restraints weight = 31145.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084710 restraints weight = 15444.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086297 restraints weight = 9310.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087385 restraints weight = 6450.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088108 restraints weight = 4879.074| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15890 Z= 0.126 Angle : 0.571 8.388 21545 Z= 0.274 Chirality : 0.046 0.203 2400 Planarity : 0.004 0.055 2720 Dihedral : 6.624 75.336 2195 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.58 % Allowed : 14.77 % Favored : 83.65 % Cbeta Deviations : 0.27 % 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: 1.18 (0.20), residues: 1900 helix: 0.91 (0.19), residues: 845 sheet: 0.08 (0.35), residues: 225 loop : 1.13 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 335 TYR 0.012 0.001 TYR D 133 PHE 0.035 0.001 PHE H 352 TRP 0.017 0.001 TRP D 340 HIS 0.002 0.001 HIS I 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (15880) covalent geometry : angle 0.57015 / 0.27 (21530) hydrogen bonds : bond 0.02762 / 1.83 ( 720) hydrogen bonds : angle 4.30419 / 2.95 ( 1755) Misc. bond : bond 0.00037 / 0.03 ( 5) link_TRANS : bond 0.00116 / 0.06 ( 5) link_TRANS : angle 1.21429 / 0.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5422 (ptt) cc_final: 0.4653 (mtm) REVERT: B 205 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7171 (mt-10) REVERT: H 44 MET cc_start: 0.7313 (mtm) cc_final: 0.7022 (mtm) REVERT: H 47 MET cc_start: 0.6321 (ttp) cc_final: 0.5037 (tmm) REVERT: E 8 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7703 (mtmt) REVERT: F 355 MET cc_start: 0.8073 (mmm) cc_final: 0.7842 (tpp) REVERT: G 9 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7582 (ttmm) REVERT: I 12 ASN cc_start: 0.7536 (m110) cc_final: 0.7251 (p0) REVERT: I 289 ILE cc_start: 0.8326 (mm) cc_final: 0.8003 (mm) outliers start: 26 outliers final: 23 residues processed: 193 average time/residue: 0.1018 time to fit residues: 30.9984 Evaluate side-chains 194 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 115 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 147 optimal weight: 0.0570 chunk 131 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN I 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.082935 restraints weight = 31053.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085368 restraints weight = 15476.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086996 restraints weight = 9371.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088075 restraints weight = 6431.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088752 restraints weight = 4856.251| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15890 Z= 0.111 Angle : 0.561 8.552 21545 Z= 0.269 Chirality : 0.045 0.200 2400 Planarity : 0.004 0.054 2720 Dihedral : 6.541 74.337 2195 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.70 % Allowed : 14.89 % Favored : 83.40 % Cbeta Deviations : 0.27 % 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: 1.23 (0.20), residues: 1900 helix: 0.99 (0.19), residues: 840 sheet: 0.04 (0.35), residues: 225 loop : 1.13 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 116 TYR 0.011 0.001 TYR F 166 PHE 0.037 0.001 PHE H 352 TRP 0.018 0.001 TRP D 340 HIS 0.002 0.001 HIS I 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (15880) covalent geometry : angle 0.56078 / 0.27 (21530) hydrogen bonds : bond 0.02647 / 1.75 ( 720) hydrogen bonds : angle 4.28370 / 2.93 ( 1755) Misc. bond : bond 0.00043 / 0.03 ( 5) link_TRANS : bond 0.00128 / 0.06 ( 5) link_TRANS : angle 1.18798 / 0.63 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5386 (ptt) cc_final: 0.4613 (mtm) REVERT: B 205 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7190 (mt-10) REVERT: H 44 MET cc_start: 0.7281 (mtm) cc_final: 0.6996 (mtm) REVERT: H 47 MET cc_start: 0.6302 (ttp) cc_final: 0.5047 (tmm) REVERT: E 8 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7720 (mtmt) REVERT: F 169 TYR cc_start: 0.8680 (m-80) cc_final: 0.8381 (m-80) REVERT: F 355 MET cc_start: 0.8077 (mmm) cc_final: 0.7804 (tpp) REVERT: G 9 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7622 (ttmm) REVERT: I 12 ASN cc_start: 0.7517 (m110) cc_final: 0.7230 (p0) REVERT: I 132 MET cc_start: 0.8673 (pmm) cc_final: 0.8239 (pmm) REVERT: I 217 CYS cc_start: 0.8303 (m) cc_final: 0.7864 (m) REVERT: I 289 ILE cc_start: 0.8286 (mm) cc_final: 0.7976 (mm) outliers start: 28 outliers final: 24 residues processed: 197 average time/residue: 0.0960 time to fit residues: 29.8939 Evaluate side-chains 196 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 115 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 150 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN B 360 GLN I 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.083011 restraints weight = 30956.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085412 restraints weight = 15471.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.087047 restraints weight = 9427.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.088154 restraints weight = 6499.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.088817 restraints weight = 4903.733| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15890 Z= 0.110 Angle : 0.564 8.470 21545 Z= 0.270 Chirality : 0.045 0.196 2400 Planarity : 0.004 0.054 2720 Dihedral : 6.487 72.886 2195 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.64 % Allowed : 14.95 % Favored : 83.40 % Cbeta Deviations : 0.27 % 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: 1.18 (0.20), residues: 1900 helix: 0.99 (0.19), residues: 840 sheet: -0.01 (0.32), residues: 265 loop : 1.12 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.024 0.001 TYR D 133 PHE 0.035 0.001 PHE H 352 TRP 0.018 0.001 TRP D 340 HIS 0.003 0.001 HIS I 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (15880) covalent geometry : angle 0.56322 / 0.27 (21530) hydrogen bonds : bond 0.02622 / 1.73 ( 720) hydrogen bonds : angle 4.25867 / 2.91 ( 1755) Misc. bond : bond 0.00042 / 0.03 ( 5) link_TRANS : bond 0.00120 / 0.06 ( 5) link_TRANS : angle 1.15161 / 0.61 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2012.44 seconds wall clock time: 35 minutes 56.40 seconds (2156.40 seconds total)