Starting phenix.real_space_refine on Wed Mar 4 19:25:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ad9_11721/03_2026/7ad9_11721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ad9_11721/03_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_11721/03_2026/7ad9_11721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ad9_11721/03_2026/7ad9_11721.map" model { file = "/net/cci-nas-00/data/ceres_data/7ad9_11721/03_2026/7ad9_11721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ad9_11721/03_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-5986/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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 Unresolved non-hydrogen dihedrals: 2 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 3.20, per 1000 atoms: 0.21 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: 1.41 Conformation dependent library (CDL) restraints added in 471.7 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: 0.78 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: 2.73 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 9335 29.01 - 58.02: 195 58.02 - 87.02: 20 87.02 - 116.03: 5 116.03 - 145.04: 10 Dihedral angle restraints: 9565 sinusoidal: 3890 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 9562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1303 0.057 - 0.115: 760 0.115 - 0.172: 218 0.172 - 0.230: 80 0.230 - 0.287: 39 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE I 151 " pdb=" CA ILE I 151 " pdb=" CG1 ILE I 151 " pdb=" CG2 ILE I 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE H 151 " pdb=" CA ILE H 151 " pdb=" CG1 ILE H 151 " pdb=" CG2 ILE H 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (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: 0.010 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.000 Find NCS groups from input model: 0.160 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.082 0.287 2400 Planarity : 0.011 0.057 2720 Dihedral : 12.965 145.040 5910 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 covalent geometry : bond 0.01667 (15880) covalent geometry : angle 1.60651 (21530) hydrogen bonds : bond 0.13841 ( 720) hydrogen bonds : angle 6.76617 ( 1755) Misc. bond : bond 0.07779 ( 5) link_TRANS : bond 0.03526 ( 5) link_TRANS : angle 3.02162 ( 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 : 0.444 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: 0.6849 (t0) REVERT: B 82 MET cc_start: 0.9072 (tpt) cc_final: 0.8851 (tpt) REVERT: B 190 MET cc_start: 0.7943 (mtp) cc_final: 0.7629 (mtp) REVERT: B 305 MET cc_start: 0.8823 (mmm) cc_final: 0.8481 (mmt) REVERT: B 326 LYS cc_start: 0.8131 (tptt) cc_final: 0.7749 (tttt) REVERT: D 82 MET cc_start: 0.8911 (tpt) cc_final: 0.8666 (tpp) REVERT: D 113 LYS cc_start: 0.7920 (mttt) cc_final: 0.7677 (mtmt) REVERT: D 115 ASN cc_start: 0.8415 (t0) cc_final: 0.8177 (t0) REVERT: D 119 MET cc_start: 0.8350 (ttp) cc_final: 0.8135 (ttm) REVERT: D 151 ILE cc_start: 0.8854 (mt) cc_final: 0.8586 (mt) REVERT: H 115 ASN cc_start: 0.8445 (t0) cc_final: 0.8077 (m-40) REVERT: F 305 MET cc_start: 0.8620 (mmm) cc_final: 0.8407 (mmp) 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: 0.7866 (m110) REVERT: I 274 ILE cc_start: 0.8022 (pt) cc_final: 0.7810 (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: 0.1290 time to fit residues: 82.1245 Evaluate side-chains 201 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 5.9990 chunk 66 optimal weight: 0.8980 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: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089175 restraints weight = 30914.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.091711 restraints weight = 15188.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.093424 restraints weight = 9078.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094534 restraints weight = 6133.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.095310 restraints weight = 4573.427| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3135 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= 0.145 Angle : 0.651 7.977 21545 Z= 0.324 Chirality : 0.047 0.178 2400 Planarity : 0.004 0.049 2720 Dihedral : 11.227 115.167 2245 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.49 % Allowed : 7.66 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1900 helix: 0.26 (0.17), residues: 840 sheet: 0.36 (0.34), residues: 235 loop : 1.34 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 372 TYR 0.016 0.001 TYR H 294 PHE 0.032 0.002 PHE D 375 TRP 0.018 0.002 TRP I 340 HIS 0.005 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00331 (15880) covalent geometry : angle 0.65128 (21530) hydrogen bonds : bond 0.03635 ( 720) hydrogen bonds : angle 4.59983 ( 1755) Misc. bond : bond 0.00102 ( 5) link_TRANS : bond 0.00106 ( 5) link_TRANS : angle 0.22102 ( 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: 41 poor density : 250 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.7316 (mmm) cc_final: 0.6986 (mmm) REVERT: B 325 MET cc_start: 0.6612 (mtm) cc_final: 0.6289 (mtt) REVERT: B 326 LYS cc_start: 0.8080 (tptt) cc_final: 0.7831 (tttt) REVERT: D 119 MET cc_start: 0.8281 (ttp) cc_final: 0.8040 (ttm) REVERT: L 11 GLU cc_start: 0.7656 (tp30) cc_final: 0.7419 (tp30) REVERT: H 115 ASN cc_start: 0.8148 (t0) cc_final: 0.7840 (m-40) REVERT: H 128 ASN cc_start: 0.7787 (m-40) cc_final: 0.7341 (t0) REVERT: H 206 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.6772 (ttp80) REVERT: H 297 ASN cc_start: 0.8419 (t0) cc_final: 0.8218 (t0) REVERT: E 6 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7962 (mm) REVERT: F 157 ASP cc_start: 0.7980 (t70) cc_final: 0.7663 (t0) REVERT: F 176 MET cc_start: 0.7984 (mmm) cc_final: 0.7769 (mmt) REVERT: F 337 TYR cc_start: 0.7432 (m-80) cc_final: 0.7223 (m-80) REVERT: F 344 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.8716 (m) REVERT: G 1 MET cc_start: 0.6001 (ptt) cc_final: 0.4840 (ptm) REVERT: G 9 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7155 (ttpp) REVERT: I 12 ASN cc_start: 0.7323 (m110) cc_final: 0.6757 (p0) REVERT: I 95 ARG cc_start: 0.7645 (mmm160) cc_final: 0.6960 (mmt180) REVERT: I 154 ASP cc_start: 0.8232 (t0) cc_final: 0.7823 (t70) REVERT: I 178 LEU cc_start: 0.8715 (mt) cc_final: 0.8514 (mt) REVERT: I 225 ASN cc_start: 0.8342 (m-40) cc_final: 0.7723 (m110) REVERT: I 289 ILE cc_start: 0.8491 (mm) cc_final: 0.8214 (mm) outliers start: 41 outliers final: 15 residues processed: 276 average time/residue: 0.1139 time to fit residues: 47.3598 Evaluate side-chains 206 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 12 ASN 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 E residue 6 LEU 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 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: 0.9990 chunk 189 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 ASN F 115 ASN I 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.080716 restraints weight = 31575.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083117 restraints weight = 15790.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.084765 restraints weight = 9648.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085832 restraints weight = 6641.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086590 restraints weight = 5053.962| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 15890 Z= 0.213 Angle : 0.663 7.527 21545 Z= 0.327 Chirality : 0.048 0.174 2400 Planarity : 0.005 0.061 2720 Dihedral : 10.048 112.990 2245 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.74 % Allowed : 10.15 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1900 helix: 0.44 (0.18), residues: 835 sheet: 0.17 (0.33), residues: 235 loop : 1.19 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 28 TYR 0.019 0.002 TYR F 198 PHE 0.022 0.002 PHE D 375 TRP 0.018 0.002 TRP D 340 HIS 0.006 0.001 HIS F 40 Details of bonding type rmsd covalent geometry : bond 0.00505 (15880) covalent geometry : angle 0.66314 (21530) hydrogen bonds : bond 0.03731 ( 720) hydrogen bonds : angle 4.75315 ( 1755) Misc. bond : bond 0.00103 ( 5) link_TRANS : bond 0.00095 ( 5) link_TRANS : angle 0.35547 ( 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 243 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 325 MET cc_start: 0.6701 (mtm) cc_final: 0.6447 (mtt) REVERT: D 47 MET cc_start: 0.7666 (ppp) cc_final: 0.7446 (tmm) REVERT: D 82 MET cc_start: 0.8791 (tpt) cc_final: 0.8527 (tpt) REVERT: D 132 MET cc_start: 0.7991 (tmm) cc_final: 0.7763 (tmm) REVERT: D 154 ASP cc_start: 0.8509 (t0) cc_final: 0.8081 (t70) REVERT: H 47 MET cc_start: 0.6487 (ttp) cc_final: 0.5410 (tmm) REVERT: H 119 MET cc_start: 0.8801 (ttm) cc_final: 0.8435 (ttm) REVERT: E 7 ILE cc_start: 0.8871 (mm) cc_final: 0.8633 (mm) REVERT: E 8 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7572 (mtmt) REVERT: F 176 MET cc_start: 0.8101 (mmm) cc_final: 0.7809 (mmt) REVERT: G 5 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8474 (p0) REVERT: G 9 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7503 (ttpp) REVERT: I 12 ASN cc_start: 0.7475 (m110) cc_final: 0.7007 (p0) REVERT: I 78 ASN cc_start: 0.6425 (t0) cc_final: 0.6123 (t0) REVERT: I 141 SER cc_start: 0.8923 (m) cc_final: 0.8697 (m) REVERT: I 154 ASP cc_start: 0.8280 (t0) cc_final: 0.7902 (t70) REVERT: I 289 ILE cc_start: 0.8612 (mm) cc_final: 0.8312 (mm) outliers start: 45 outliers final: 23 residues processed: 231 average time/residue: 0.1056 time to fit residues: 38.0750 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 : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL 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 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 H residue 132 MET 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 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 G residue 5 ASP 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: 1.9990 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3220 r_free = 0.3220 target = 0.092762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.082043 restraints weight = 31331.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.084484 restraints weight = 15511.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.086138 restraints weight = 9356.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087235 restraints weight = 6379.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.087994 restraints weight = 4770.532| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 15890 Z= 0.140 Angle : 0.587 7.827 21545 Z= 0.283 Chirality : 0.046 0.162 2400 Planarity : 0.004 0.059 2720 Dihedral : 9.192 105.866 2245 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.31 % Allowed : 11.25 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.19), residues: 1900 helix: 0.63 (0.18), residues: 840 sheet: 0.14 (0.34), residues: 235 loop : 1.26 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.011 0.001 TYR I 294 PHE 0.013 0.002 PHE D 352 TRP 0.021 0.002 TRP D 340 HIS 0.004 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00332 (15880) covalent geometry : angle 0.58756 (21530) hydrogen bonds : bond 0.02986 ( 720) hydrogen bonds : angle 4.52792 ( 1755) Misc. bond : bond 0.00044 ( 5) link_TRANS : bond 0.00073 ( 5) link_TRANS : angle 0.19882 ( 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 232 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: B 205 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7269 (mt-10) REVERT: H 47 MET cc_start: 0.6428 (ttp) cc_final: 0.5280 (tmm) REVERT: H 346 LEU cc_start: 0.9473 (tp) cc_final: 0.9198 (tp) REVERT: E 8 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7716 (mtmt) REVERT: G 9 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7316 (ttmm) REVERT: I 12 ASN cc_start: 0.7309 (m110) cc_final: 0.6857 (p0) REVERT: I 154 ASP cc_start: 0.8380 (t0) cc_final: 0.8124 (t70) REVERT: I 289 ILE cc_start: 0.8574 (mm) cc_final: 0.8274 (mm) REVERT: I 300 SER cc_start: 0.8213 (p) cc_final: 0.8006 (m) outliers start: 38 outliers final: 24 residues processed: 219 average time/residue: 0.1085 time to fit residues: 36.8666 Evaluate side-chains 190 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 297 ASN 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 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 6 THR 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: 5.9990 chunk 53 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN H 297 ASN F 115 ASN I 78 ASN I 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.092048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081429 restraints weight = 31458.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.083843 restraints weight = 15485.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085476 restraints weight = 9355.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.086559 restraints weight = 6371.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087285 restraints weight = 4787.207| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15890 Z= 0.150 Angle : 0.586 7.206 21545 Z= 0.282 Chirality : 0.046 0.180 2400 Planarity : 0.004 0.062 2720 Dihedral : 8.322 91.926 2245 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.13 % Allowed : 12.16 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.20), residues: 1900 helix: 0.68 (0.19), residues: 845 sheet: 0.25 (0.35), residues: 225 loop : 1.17 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 335 TYR 0.015 0.001 TYR I 294 PHE 0.022 0.002 PHE H 375 TRP 0.016 0.001 TRP D 340 HIS 0.003 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00354 (15880) covalent geometry : angle 0.58570 (21530) hydrogen bonds : bond 0.03021 ( 720) hydrogen bonds : angle 4.48993 ( 1755) Misc. bond : bond 0.00044 ( 5) link_TRANS : bond 0.00098 ( 5) link_TRANS : angle 0.23231 ( 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 208 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5847 (ptt) cc_final: 0.5383 (ptm) REVERT: B 205 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7222 (mt-10) REVERT: D 283 MET cc_start: 0.8687 (mmm) cc_final: 0.8457 (mmp) REVERT: H 47 MET cc_start: 0.6391 (ttp) cc_final: 0.5254 (tmm) REVERT: H 194 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8756 (p) REVERT: H 355 MET cc_start: 0.7840 (mtp) cc_final: 0.7518 (mtt) REVERT: E 8 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7761 (mtmt) REVERT: F 313 MET cc_start: 0.8789 (tpp) cc_final: 0.8558 (ttm) REVERT: G 9 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7437 (ttmm) REVERT: I 12 ASN cc_start: 0.7437 (m110) cc_final: 0.7009 (p0) REVERT: I 154 ASP cc_start: 0.8297 (t0) cc_final: 0.8049 (t70) REVERT: I 289 ILE cc_start: 0.8565 (mm) cc_final: 0.8272 (mm) REVERT: I 300 SER cc_start: 0.8150 (p) cc_final: 0.7938 (m) outliers start: 35 outliers final: 25 residues processed: 194 average time/residue: 0.1048 time to fit residues: 31.8719 Evaluate side-chains 189 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE 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 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 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 6 THR Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 250 ILE 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: 0.9980 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 5 optimal weight: 0.0050 chunk 3 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.092166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.081604 restraints weight = 31332.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.084038 restraints weight = 15448.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085642 restraints weight = 9244.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.086629 restraints weight = 6318.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.087394 restraints weight = 4847.403| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15890 Z= 0.135 Angle : 0.562 6.628 21545 Z= 0.270 Chirality : 0.045 0.165 2400 Planarity : 0.004 0.057 2720 Dihedral : 7.664 84.228 2245 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.19 % Allowed : 12.83 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1900 helix: 0.78 (0.19), residues: 845 sheet: 0.14 (0.35), residues: 225 loop : 1.14 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 335 TYR 0.014 0.001 TYR D 133 PHE 0.017 0.002 PHE D 352 TRP 0.016 0.001 TRP D 340 HIS 0.003 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00319 (15880) covalent geometry : angle 0.56228 (21530) hydrogen bonds : bond 0.02831 ( 720) hydrogen bonds : angle 4.41903 ( 1755) Misc. bond : bond 0.00036 ( 5) link_TRANS : bond 0.00096 ( 5) link_TRANS : angle 0.20754 ( 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 206 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5632 (ptt) cc_final: 0.4641 (mtm) REVERT: B 137 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: B 205 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7164 (mt-10) REVERT: H 47 MET cc_start: 0.6310 (ttp) cc_final: 0.5188 (tmm) REVERT: H 355 MET cc_start: 0.7842 (mtp) cc_final: 0.7617 (mtt) REVERT: E 8 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7776 (mtmt) REVERT: F 132 MET cc_start: 0.7592 (ttp) cc_final: 0.7244 (ptm) REVERT: F 313 MET cc_start: 0.8754 (tpp) cc_final: 0.8508 (ttm) REVERT: G 9 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7457 (ttmm) REVERT: I 12 ASN cc_start: 0.7594 (m110) cc_final: 0.7146 (p0) REVERT: I 137 GLN cc_start: 0.8388 (mp10) cc_final: 0.8121 (mt0) REVERT: I 289 ILE cc_start: 0.8502 (mm) cc_final: 0.8229 (mm) REVERT: I 300 SER cc_start: 0.8085 (p) cc_final: 0.7861 (m) outliers start: 36 outliers final: 27 residues processed: 194 average time/residue: 0.0994 time to fit residues: 30.8514 Evaluate side-chains 187 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain B residue 137 GLN 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 B residue 372 ARG Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET 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 G residue 12 SER Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 250 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: 0.6980 chunk 123 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 157 optimal weight: 0.0470 chunk 163 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3229 r_free = 0.3229 target = 0.093429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.082888 restraints weight = 31057.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085370 restraints weight = 15251.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.086977 restraints weight = 9081.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.088059 restraints weight = 6175.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088798 restraints weight = 4624.400| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15890 Z= 0.104 Angle : 0.546 8.237 21545 Z= 0.260 Chirality : 0.044 0.186 2400 Planarity : 0.004 0.054 2720 Dihedral : 7.321 83.853 2245 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.88 % Allowed : 13.62 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.25 (0.20), residues: 1900 helix: 0.92 (0.19), residues: 845 sheet: 0.15 (0.35), residues: 225 loop : 1.20 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 335 TYR 0.015 0.001 TYR D 133 PHE 0.017 0.001 PHE H 375 TRP 0.015 0.001 TRP D 340 HIS 0.004 0.001 HIS F 371 Details of bonding type rmsd covalent geometry : bond 0.00242 (15880) covalent geometry : angle 0.54667 (21530) hydrogen bonds : bond 0.02626 ( 720) hydrogen bonds : angle 4.32127 ( 1755) Misc. bond : bond 0.00033 ( 5) link_TRANS : bond 0.00029 ( 5) link_TRANS : angle 0.18603 ( 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 209 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5516 (ptt) cc_final: 0.4627 (mtm) REVERT: B 205 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7048 (mt-10) REVERT: L 13 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8419 (tt) REVERT: H 47 MET cc_start: 0.6305 (ttp) cc_final: 0.5160 (tmm) REVERT: H 355 MET cc_start: 0.7733 (mtp) cc_final: 0.7519 (mtt) REVERT: E 8 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7661 (mtmt) REVERT: F 313 MET cc_start: 0.8733 (tpp) cc_final: 0.8484 (ttm) REVERT: G 9 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7589 (ttmm) REVERT: I 12 ASN cc_start: 0.7587 (m110) cc_final: 0.7166 (p0) REVERT: I 56 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8247 (t0) REVERT: I 132 MET cc_start: 0.8573 (pmm) cc_final: 0.7836 (pmm) REVERT: I 289 ILE cc_start: 0.8380 (mm) cc_final: 0.8100 (mm) outliers start: 31 outliers final: 19 residues processed: 199 average time/residue: 0.1007 time to fit residues: 31.7312 Evaluate side-chains 180 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 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 L residue 13 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET 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 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ASP 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: 0.7980 chunk 117 optimal weight: 0.3980 chunk 157 optimal weight: 0.0370 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN F 115 ASN I 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.093935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.083402 restraints weight = 31458.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.085832 restraints weight = 15367.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087475 restraints weight = 9200.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.088548 restraints weight = 6243.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089284 restraints weight = 4679.630| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5317 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= 0.100 Angle : 0.548 9.006 21545 Z= 0.260 Chirality : 0.044 0.158 2400 Planarity : 0.004 0.055 2720 Dihedral : 7.133 83.423 2245 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.88 % Allowed : 13.92 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1900 helix: 0.99 (0.19), residues: 845 sheet: 0.14 (0.35), residues: 225 loop : 1.23 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 335 TYR 0.017 0.001 TYR D 133 PHE 0.020 0.001 PHE D 352 TRP 0.016 0.001 TRP D 340 HIS 0.002 0.001 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00234 (15880) covalent geometry : angle 0.54782 (21530) hydrogen bonds : bond 0.02571 ( 720) hydrogen bonds : angle 4.26887 ( 1755) Misc. bond : bond 0.00030 ( 5) link_TRANS : bond 0.00019 ( 5) link_TRANS : angle 0.17741 ( 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 202 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5363 (ptt) cc_final: 0.4621 (mtm) REVERT: B 205 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7083 (mt-10) REVERT: H 47 MET cc_start: 0.6290 (ttp) cc_final: 0.5143 (tmm) REVERT: H 194 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8742 (p) REVERT: H 355 MET cc_start: 0.7852 (mtp) cc_final: 0.7618 (mtt) REVERT: E 8 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7711 (mtmt) REVERT: F 123 MET cc_start: 0.8090 (mmt) cc_final: 0.7882 (mmt) REVERT: F 313 MET cc_start: 0.8707 (tpp) cc_final: 0.8472 (ttm) REVERT: G 9 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7670 (ttmm) REVERT: I 12 ASN cc_start: 0.7592 (m110) cc_final: 0.7201 (p0) REVERT: I 56 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8289 (t0) REVERT: I 289 ILE cc_start: 0.8384 (mm) cc_final: 0.8114 (mm) outliers start: 31 outliers final: 20 residues processed: 192 average time/residue: 0.1057 time to fit residues: 31.5525 Evaluate side-chains 186 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 119 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain H residue 132 MET 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 35 VAL Chi-restraints excluded: chain I residue 56 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 0.0060 chunk 101 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 105 optimal weight: 0.0050 chunk 148 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084599 restraints weight = 31222.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.087068 restraints weight = 15288.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.088698 restraints weight = 9078.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089765 restraints weight = 6161.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.090509 restraints weight = 4615.554| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5415 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= 0.092 Angle : 0.542 9.053 21545 Z= 0.258 Chirality : 0.044 0.157 2400 Planarity : 0.004 0.054 2720 Dihedral : 6.961 82.148 2245 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.76 % Allowed : 14.16 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1900 helix: 1.11 (0.19), residues: 840 sheet: 0.11 (0.35), residues: 225 loop : 1.23 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 335 TYR 0.013 0.001 TYR H 306 PHE 0.017 0.001 PHE D 352 TRP 0.016 0.001 TRP D 340 HIS 0.003 0.001 HIS I 161 Details of bonding type rmsd covalent geometry : bond 0.00215 (15880) covalent geometry : angle 0.54254 (21530) hydrogen bonds : bond 0.02422 ( 720) hydrogen bonds : angle 4.21635 ( 1755) Misc. bond : bond 0.00032 ( 5) link_TRANS : bond 0.00029 ( 5) link_TRANS : angle 0.16355 ( 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 214 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5249 (ptt) cc_final: 0.4494 (mtm) REVERT: B 205 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7191 (mt-10) REVERT: H 47 MET cc_start: 0.6279 (ttp) cc_final: 0.5152 (tmm) REVERT: H 355 MET cc_start: 0.7809 (mtp) cc_final: 0.7596 (mtt) REVERT: E 8 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7632 (mtmt) REVERT: F 123 MET cc_start: 0.8012 (mmt) cc_final: 0.7799 (mmt) REVERT: F 313 MET cc_start: 0.8710 (tpp) cc_final: 0.8454 (ttm) REVERT: F 355 MET cc_start: 0.8126 (mmm) cc_final: 0.7838 (tpp) REVERT: I 12 ASN cc_start: 0.7597 (m110) cc_final: 0.7201 (p0) REVERT: I 56 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8181 (t0) REVERT: I 289 ILE cc_start: 0.8285 (mm) cc_final: 0.8023 (mm) outliers start: 29 outliers final: 22 residues processed: 204 average time/residue: 0.1070 time to fit residues: 33.8168 Evaluate side-chains 194 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 115 ASN Chi-restraints excluded: chain B residue 119 MET 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 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 7 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 250 ILE 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: 5.9990 chunk 17 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 147 optimal weight: 0.0170 chunk 131 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.081658 restraints weight = 31505.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084095 restraints weight = 15484.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085710 restraints weight = 9289.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086777 restraints weight = 6331.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087438 restraints weight = 4765.258| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15890 Z= 0.148 Angle : 0.584 8.862 21545 Z= 0.281 Chirality : 0.046 0.160 2400 Planarity : 0.004 0.055 2720 Dihedral : 7.118 83.195 2245 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.70 % Allowed : 14.71 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1900 helix: 0.93 (0.19), residues: 845 sheet: -0.01 (0.32), residues: 265 loop : 1.21 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 335 TYR 0.024 0.001 TYR D 133 PHE 0.015 0.002 PHE H 375 TRP 0.018 0.001 TRP D 340 HIS 0.003 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00353 (15880) covalent geometry : angle 0.58436 (21530) hydrogen bonds : bond 0.02824 ( 720) hydrogen bonds : angle 4.31109 ( 1755) Misc. bond : bond 0.00017 ( 5) link_TRANS : bond 0.00136 ( 5) link_TRANS : angle 0.26350 ( 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 200 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5381 (ptt) cc_final: 0.4655 (mtm) REVERT: B 205 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7192 (mt-10) REVERT: D 353 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7677 (mm110) REVERT: H 47 MET cc_start: 0.6118 (ttp) cc_final: 0.5273 (tmm) REVERT: H 355 MET cc_start: 0.7920 (mtp) cc_final: 0.7681 (mtt) REVERT: E 8 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7700 (mtmt) REVERT: F 313 MET cc_start: 0.8750 (tpp) cc_final: 0.8494 (ttm) REVERT: F 355 MET cc_start: 0.8015 (mmm) cc_final: 0.7708 (tpt) REVERT: I 12 ASN cc_start: 0.7731 (m110) cc_final: 0.7325 (p0) REVERT: I 217 CYS cc_start: 0.8278 (m) cc_final: 0.8024 (m) REVERT: I 289 ILE cc_start: 0.8514 (mm) cc_final: 0.8268 (mm) outliers start: 28 outliers final: 23 residues processed: 190 average time/residue: 0.0983 time to fit residues: 29.6652 Evaluate side-chains 189 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 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 I residue 30 VAL Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 287 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 150 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 57 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 33 optimal weight: 0.0020 chunk 109 optimal weight: 4.9990 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS B 115 ASN B 246 GLN B 360 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.084396 restraints weight = 31070.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086856 restraints weight = 15280.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088466 restraints weight = 9099.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089536 restraints weight = 6202.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.090253 restraints weight = 4656.639| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.5566 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= 0.096 Angle : 0.561 14.570 21545 Z= 0.266 Chirality : 0.044 0.155 2400 Planarity : 0.004 0.053 2720 Dihedral : 6.943 81.531 2245 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.34 % Allowed : 15.14 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1900 helix: 1.11 (0.19), residues: 840 sheet: -0.04 (0.32), residues: 265 loop : 1.22 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 335 TYR 0.029 0.001 TYR D 133 PHE 0.016 0.001 PHE D 352 TRP 0.018 0.001 TRP D 340 HIS 0.003 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00226 (15880) covalent geometry : angle 0.56119 (21530) hydrogen bonds : bond 0.02462 ( 720) hydrogen bonds : angle 4.20219 ( 1755) Misc. bond : bond 0.00036 ( 5) link_TRANS : bond 0.00024 ( 5) link_TRANS : angle 0.23600 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.77 seconds wall clock time: 35 minutes 40.29 seconds (2140.29 seconds total)