Starting phenix.real_space_refine on Mon Jul 22 09:27:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/07_2024/7uxf_26860_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/07_2024/7uxf_26860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/07_2024/7uxf_26860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/07_2024/7uxf_26860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/07_2024/7uxf_26860_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uxf_26860/07_2024/7uxf_26860_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.049 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 12 5.49 5 Mg 6 5.21 5 S 126 5.16 5 C 11028 2.51 5 N 2958 2.21 5 O 3426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E ARG 372": "NH1" <-> "NH2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 214": "OE1" <-> "OE2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "F ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17556 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 10.34, per 1000 atoms: 0.59 Number of scatterers: 17556 At special positions: 0 Unit cell: (89.134, 97.83, 219.574, 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 126 16.00 P 12 15.00 Mg 6 11.99 O 3426 8.00 N 2958 7.00 C 11028 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 3.5 seconds 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 36 sheets defined 52.8% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.639A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.835A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.262A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.741A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.638A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.834A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 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 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.740A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.639A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.835A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.786A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.740A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.638A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.835A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 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 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.741A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.639A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.835A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.740A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 364 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.638A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.835A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.787A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 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 305 Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.740A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 364 Processing helix chain 'F' and resid 366 through 368 No H-bonds generated for 'chain 'F' and resid 366 through 368' Processing helix chain 'F' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.696A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.799A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.799A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.697A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.795A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.795A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB7, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.696A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.795A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.795A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.696A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.799A pdb=" N GLN D 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.799A pdb=" N GLN D 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.696A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD4, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD6, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.696A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD8, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 915 hydrogen bonds defined for protein. 2331 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: 6.93 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5483 1.33 - 1.46: 3158 1.46 - 1.58: 8993 1.58 - 1.70: 18 1.70 - 1.82: 222 Bond restraints: 17874 Sorted by residual: bond pdb=" N VAL F 159 " pdb=" CA VAL F 159 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.14e-02 7.69e+03 1.44e+01 bond pdb=" N VAL D 159 " pdb=" CA VAL D 159 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.14e-02 7.69e+03 1.41e+01 bond pdb=" N VAL E 159 " pdb=" CA VAL E 159 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.18e-02 7.18e+03 1.15e+01 ... (remaining 17869 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.54: 463 105.54 - 113.21: 9783 113.21 - 120.88: 8667 120.88 - 128.55: 5231 128.55 - 136.22: 114 Bond angle restraints: 24258 Sorted by residual: angle pdb=" C THR A 303 " pdb=" CA THR A 303 " pdb=" CB THR A 303 " ideal model delta sigma weight residual 109.99 119.47 -9.48 2.09e+00 2.29e-01 2.06e+01 angle pdb=" N ILE D 151 " pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 107.80 101.81 5.99 1.45e+00 4.76e-01 1.70e+01 angle pdb=" C ILE D 151 " pdb=" N VAL D 152 " pdb=" CA VAL D 152 " ideal model delta sigma weight residual 123.19 118.35 4.84 1.24e+00 6.50e-01 1.52e+01 angle pdb=" N THR A 303 " pdb=" CA THR A 303 " pdb=" C THR A 303 " ideal model delta sigma weight residual 112.89 108.06 4.83 1.24e+00 6.50e-01 1.52e+01 angle pdb=" CA GLY D 150 " pdb=" C GLY D 150 " pdb=" O GLY D 150 " ideal model delta sigma weight residual 121.37 117.70 3.67 1.09e+00 8.42e-01 1.14e+01 ... (remaining 24253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 9920 20.59 - 41.18: 683 41.18 - 61.77: 125 61.77 - 82.36: 24 82.36 - 102.95: 6 Dihedral angle restraints: 10758 sinusoidal: 4344 harmonic: 6414 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.95 -102.95 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.91 -102.91 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 42.90 -102.90 1 2.00e+01 2.50e-03 2.94e+01 ... (remaining 10755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1939 0.054 - 0.108: 643 0.108 - 0.161: 97 0.161 - 0.215: 13 0.215 - 0.269: 8 Chirality restraints: 2700 Sorted by residual: chirality pdb=" CB VAL F 159 " pdb=" CA VAL F 159 " pdb=" CG1 VAL F 159 " pdb=" CG2 VAL F 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL D 159 " pdb=" CA VAL D 159 " pdb=" CG1 VAL D 159 " pdb=" CG2 VAL D 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL B 159 " pdb=" CA VAL B 159 " pdb=" CG1 VAL B 159 " pdb=" CG2 VAL B 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2697 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 156 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C GLY A 156 " -0.070 2.00e-02 2.50e+03 pdb=" O GLY A 156 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP A 157 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 156 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLY F 156 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY F 156 " -0.026 2.00e-02 2.50e+03 pdb=" N ASP F 157 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 156 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY E 156 " -0.068 2.00e-02 2.50e+03 pdb=" O GLY E 156 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP E 157 " 0.024 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 86 2.57 - 3.15: 13646 3.15 - 3.73: 28005 3.73 - 4.32: 42552 4.32 - 4.90: 69765 Nonbonded interactions: 154054 Sorted by model distance: nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 1.983 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.990 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.997 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.015 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.019 2.170 ... (remaining 154049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 50.590 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.008 0.051 17874 Z= 0.503 Angle : 0.805 9.477 24258 Z= 0.442 Chirality : 0.054 0.269 2700 Planarity : 0.006 0.060 3096 Dihedral : 14.773 102.947 6654 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.71 % Allowed : 3.15 % Favored : 95.14 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2190 helix: -0.00 (0.18), residues: 870 sheet: 0.38 (0.24), residues: 414 loop : 0.49 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.009 0.001 HIS D 161 PHE 0.006 0.001 PHE E 262 TYR 0.014 0.001 TYR D 143 ARG 0.009 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 275 time to evaluate : 2.078 Fit side-chains REVERT: A 299 MET cc_start: 0.8577 (mtm) cc_final: 0.8280 (mtm) REVERT: A 305 MET cc_start: 0.8891 (mmm) cc_final: 0.8659 (mmp) REVERT: B 25 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6920 (p0) REVERT: B 51 ASP cc_start: 0.7822 (p0) cc_final: 0.7584 (p0) REVERT: B 92 ASN cc_start: 0.9011 (m-40) cc_final: 0.8793 (m110) REVERT: B 119 MET cc_start: 0.8154 (mtm) cc_final: 0.7914 (mtp) REVERT: B 123 MET cc_start: 0.8806 (mmt) cc_final: 0.8329 (mmp) REVERT: B 283 MET cc_start: 0.9134 (mmm) cc_final: 0.8865 (mmm) REVERT: C 25 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7391 (p0) REVERT: C 116 ARG cc_start: 0.8393 (ttm170) cc_final: 0.8190 (ttm170) REVERT: C 123 MET cc_start: 0.9002 (mmt) cc_final: 0.8558 (mmt) REVERT: C 359 LYS cc_start: 0.7762 (tptp) cc_final: 0.7490 (tptt) REVERT: D 153 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8468 (tp) REVERT: E 83 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7223 (mt-10) REVERT: E 132 MET cc_start: 0.8395 (ppp) cc_final: 0.8178 (ppp) REVERT: E 325 MET cc_start: 0.8642 (mmp) cc_final: 0.8222 (mmp) REVERT: E 355 MET cc_start: 0.8294 (mtt) cc_final: 0.7980 (mtp) REVERT: F 153 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8794 (tt) outliers start: 32 outliers final: 6 residues processed: 305 average time/residue: 1.8039 time to fit residues: 600.2012 Evaluate side-chains 195 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 246 GLN B 41 GLN B 353 GLN C 41 GLN C 225 ASN C 246 GLN C 353 GLN C 354 GLN D 161 HIS D 225 ASN D 353 GLN E 225 ASN E 314 GLN E 353 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17874 Z= 0.209 Angle : 0.596 7.005 24258 Z= 0.294 Chirality : 0.045 0.137 2700 Planarity : 0.005 0.042 3096 Dihedral : 7.525 100.018 2505 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.66 % Allowed : 8.71 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.19), residues: 2190 helix: 0.50 (0.18), residues: 894 sheet: 0.63 (0.23), residues: 408 loop : 0.88 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.004 0.001 HIS D 161 PHE 0.007 0.001 PHE F 127 TYR 0.013 0.001 TYR D 143 ARG 0.005 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 216 time to evaluate : 2.020 Fit side-chains REVERT: A 95 ARG cc_start: 0.7412 (mtt90) cc_final: 0.7202 (mtt90) REVERT: B 25 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6975 (p0) REVERT: B 51 ASP cc_start: 0.7814 (p0) cc_final: 0.7584 (p0) REVERT: B 72 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: B 123 MET cc_start: 0.8783 (mmt) cc_final: 0.8251 (mmm) REVERT: B 283 MET cc_start: 0.9060 (mmm) cc_final: 0.8810 (mmm) REVERT: C 72 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: C 123 MET cc_start: 0.8887 (mmt) cc_final: 0.8544 (mmt) REVERT: C 314 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: C 372 ARG cc_start: 0.8279 (ptp90) cc_final: 0.8019 (ptp-170) REVERT: D 72 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6985 (tm-30) REVERT: D 314 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: E 123 MET cc_start: 0.8966 (mmp) cc_final: 0.8703 (mmt) REVERT: E 132 MET cc_start: 0.8323 (ppp) cc_final: 0.8106 (ppp) REVERT: E 355 MET cc_start: 0.8101 (mtt) cc_final: 0.7796 (mtp) REVERT: F 95 ARG cc_start: 0.7682 (mtt-85) cc_final: 0.7450 (mtt90) REVERT: F 122 ILE cc_start: 0.8482 (mt) cc_final: 0.8178 (mp) REVERT: F 326 LYS cc_start: 0.8144 (tppt) cc_final: 0.7884 (mptt) outliers start: 31 outliers final: 11 residues processed: 231 average time/residue: 1.5372 time to fit residues: 390.6109 Evaluate side-chains 200 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN B 41 GLN B 296 ASN B 353 GLN C 41 GLN C 115 ASN C 225 ASN C 296 ASN D 115 ASN D 225 ASN D 296 ASN E 246 GLN F 115 ASN F 314 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17874 Z= 0.419 Angle : 0.666 7.604 24258 Z= 0.329 Chirality : 0.050 0.151 2700 Planarity : 0.005 0.040 3096 Dihedral : 7.555 106.085 2498 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.76 % Allowed : 10.74 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2190 helix: 0.45 (0.18), residues: 894 sheet: 0.49 (0.24), residues: 402 loop : 0.69 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.002 PHE F 127 TYR 0.016 0.002 TYR C 188 ARG 0.005 0.001 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.884 Fit side-chains REVERT: A 364 GLU cc_start: 0.8145 (pp20) cc_final: 0.7822 (tm-30) REVERT: B 25 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7090 (p0) REVERT: B 51 ASP cc_start: 0.7797 (p0) cc_final: 0.7570 (p0) REVERT: B 72 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: B 82 MET cc_start: 0.8665 (tpt) cc_final: 0.8456 (tpt) REVERT: B 123 MET cc_start: 0.8823 (mmt) cc_final: 0.8360 (mmm) REVERT: C 72 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6817 (tm-30) REVERT: C 123 MET cc_start: 0.8909 (mmt) cc_final: 0.8494 (mmt) REVERT: C 276 GLU cc_start: 0.7685 (tt0) cc_final: 0.7476 (tt0) REVERT: C 314 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: D 72 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: D 227 MET cc_start: 0.8621 (mmm) cc_final: 0.8219 (mmm) REVERT: D 314 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: D 372 ARG cc_start: 0.8254 (ptp90) cc_final: 0.8012 (ptt-90) REVERT: E 72 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: E 132 MET cc_start: 0.8352 (ppp) cc_final: 0.8088 (ppp) REVERT: E 355 MET cc_start: 0.8099 (mtt) cc_final: 0.7824 (mtp) REVERT: F 47 MET cc_start: 0.6741 (mtm) cc_final: 0.6072 (mtp) REVERT: F 95 ARG cc_start: 0.7765 (mtt-85) cc_final: 0.7505 (mtm-85) outliers start: 33 outliers final: 20 residues processed: 211 average time/residue: 1.6037 time to fit residues: 371.0141 Evaluate side-chains 208 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 41 GLN D 225 ASN D 297 ASN E 225 ASN E 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 17874 Z= 0.317 Angle : 0.609 8.229 24258 Z= 0.299 Chirality : 0.047 0.149 2700 Planarity : 0.005 0.040 3096 Dihedral : 7.374 105.012 2498 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.19 % Allowed : 11.70 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2190 helix: 0.56 (0.18), residues: 894 sheet: 0.52 (0.25), residues: 402 loop : 0.68 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.009 0.001 PHE F 127 TYR 0.011 0.001 TYR C 188 ARG 0.005 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 2.024 Fit side-chains REVERT: A 99 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 364 GLU cc_start: 0.8004 (pp20) cc_final: 0.7696 (tm-30) REVERT: B 25 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7061 (p0) REVERT: B 51 ASP cc_start: 0.7784 (p0) cc_final: 0.7541 (p0) REVERT: B 57 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: B 72 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: B 132 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8180 (ptm) REVERT: C 72 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: C 123 MET cc_start: 0.8870 (mmt) cc_final: 0.8458 (mmt) REVERT: C 276 GLU cc_start: 0.7676 (tt0) cc_final: 0.7474 (tt0) REVERT: C 314 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: C 372 ARG cc_start: 0.8337 (ptp-170) cc_final: 0.7907 (ptp-170) REVERT: D 72 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: D 153 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8654 (tp) REVERT: D 314 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: D 372 ARG cc_start: 0.8268 (ptp90) cc_final: 0.7976 (ptt-90) REVERT: E 72 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7180 (mt-10) REVERT: E 132 MET cc_start: 0.8319 (ppp) cc_final: 0.8047 (ppp) REVERT: E 355 MET cc_start: 0.8097 (mtt) cc_final: 0.7815 (mtp) REVERT: E 364 GLU cc_start: 0.7613 (pp20) cc_final: 0.7264 (tm-30) REVERT: F 47 MET cc_start: 0.6668 (mtm) cc_final: 0.5966 (mtp) REVERT: F 50 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7227 (mttm) outliers start: 41 outliers final: 23 residues processed: 223 average time/residue: 1.6011 time to fit residues: 391.3083 Evaluate side-chains 223 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 41 GLN D 225 ASN E 225 ASN E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17874 Z= 0.222 Angle : 0.569 8.198 24258 Z= 0.277 Chirality : 0.045 0.142 2700 Planarity : 0.004 0.038 3096 Dihedral : 7.144 103.950 2498 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.30 % Allowed : 12.34 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2190 helix: 0.73 (0.18), residues: 900 sheet: 0.66 (0.25), residues: 390 loop : 0.70 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 255 TYR 0.010 0.001 TYR D 69 ARG 0.006 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 192 time to evaluate : 1.945 Fit side-chains REVERT: A 328 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7675 (mtpp) REVERT: A 364 GLU cc_start: 0.7992 (pp20) cc_final: 0.7637 (tm-30) REVERT: B 25 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7071 (p0) REVERT: B 51 ASP cc_start: 0.7783 (p0) cc_final: 0.7550 (p0) REVERT: B 57 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: B 132 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8079 (ptm) REVERT: B 276 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: B 364 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7272 (pp20) REVERT: C 72 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: C 123 MET cc_start: 0.8848 (mmt) cc_final: 0.8437 (mmt) REVERT: C 314 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: C 372 ARG cc_start: 0.8383 (ptp-170) cc_final: 0.7994 (ptp-170) REVERT: D 72 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: D 153 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8658 (tp) REVERT: D 227 MET cc_start: 0.8479 (mmm) cc_final: 0.7893 (mmm) REVERT: D 314 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: D 372 ARG cc_start: 0.8260 (ptp90) cc_final: 0.7968 (ptt-90) REVERT: E 132 MET cc_start: 0.8275 (ppp) cc_final: 0.7963 (ppp) REVERT: E 355 MET cc_start: 0.8095 (mtt) cc_final: 0.7824 (mtp) REVERT: E 364 GLU cc_start: 0.7565 (pp20) cc_final: 0.7309 (tm-30) REVERT: F 47 MET cc_start: 0.6352 (mtm) cc_final: 0.5962 (mtp) REVERT: F 50 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7191 (mttm) outliers start: 43 outliers final: 20 residues processed: 220 average time/residue: 1.5984 time to fit residues: 385.3679 Evaluate side-chains 219 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 161 HIS C 353 GLN D 225 ASN F 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17874 Z= 0.345 Angle : 0.615 10.294 24258 Z= 0.302 Chirality : 0.048 0.151 2700 Planarity : 0.005 0.039 3096 Dihedral : 7.218 104.302 2496 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.30 % Allowed : 12.77 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2190 helix: 0.63 (0.18), residues: 900 sheet: 0.63 (0.25), residues: 390 loop : 0.65 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE F 127 TYR 0.011 0.001 TYR C 188 ARG 0.007 0.001 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 2.007 Fit side-chains REVERT: A 72 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: A 328 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7377 (mtpp) REVERT: A 364 GLU cc_start: 0.8034 (pp20) cc_final: 0.7675 (tm-30) REVERT: B 25 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7034 (p0) REVERT: B 51 ASP cc_start: 0.7768 (p0) cc_final: 0.7561 (p0) REVERT: B 57 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: B 72 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7125 (tp30) REVERT: B 132 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8161 (ptm) REVERT: B 276 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: B 364 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7321 (pp20) REVERT: C 72 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: C 123 MET cc_start: 0.8847 (mmt) cc_final: 0.8444 (mmt) REVERT: C 314 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7681 (tm-30) REVERT: C 372 ARG cc_start: 0.8510 (ptp-170) cc_final: 0.8131 (ptp-170) REVERT: D 72 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: D 153 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8672 (tp) REVERT: D 227 MET cc_start: 0.8546 (mmm) cc_final: 0.7926 (mmm) REVERT: D 314 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: D 372 ARG cc_start: 0.8287 (ptp90) cc_final: 0.7970 (ptt-90) REVERT: E 132 MET cc_start: 0.8303 (ppp) cc_final: 0.7986 (ppp) REVERT: E 355 MET cc_start: 0.8102 (mtt) cc_final: 0.7832 (mtp) REVERT: F 47 MET cc_start: 0.6163 (mtm) cc_final: 0.5825 (mtp) REVERT: F 50 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7193 (mttm) REVERT: F 349 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7869 (mp) outliers start: 43 outliers final: 24 residues processed: 221 average time/residue: 1.6594 time to fit residues: 400.9147 Evaluate side-chains 228 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 0.0970 chunk 180 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 213 optimal weight: 0.0770 chunk 133 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 overall best weight: 0.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 225 ASN E 225 ASN E 246 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17874 Z= 0.158 Angle : 0.536 9.811 24258 Z= 0.259 Chirality : 0.044 0.135 2700 Planarity : 0.004 0.036 3096 Dihedral : 6.752 101.329 2496 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.66 % Allowed : 13.68 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2190 helix: 0.96 (0.18), residues: 900 sheet: 0.74 (0.26), residues: 390 loop : 0.78 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 255 TYR 0.009 0.001 TYR D 69 ARG 0.006 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 2.009 Fit side-chains REVERT: A 328 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7376 (mtpp) REVERT: A 364 GLU cc_start: 0.8037 (pp20) cc_final: 0.7646 (tm-30) REVERT: B 25 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7099 (p0) REVERT: B 51 ASP cc_start: 0.7754 (p0) cc_final: 0.7550 (p0) REVERT: B 123 MET cc_start: 0.8751 (mmt) cc_final: 0.8146 (mmp) REVERT: B 132 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8031 (ptm) REVERT: B 276 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: C 72 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6744 (tm-30) REVERT: C 123 MET cc_start: 0.8801 (mmt) cc_final: 0.8466 (mmt) REVERT: C 372 ARG cc_start: 0.8517 (ptp-170) cc_final: 0.8149 (ptp-170) REVERT: D 72 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: D 80 ASP cc_start: 0.7985 (m-30) cc_final: 0.7592 (m-30) REVERT: D 153 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8634 (tp) REVERT: D 227 MET cc_start: 0.8554 (mmm) cc_final: 0.7923 (mmm) REVERT: E 132 MET cc_start: 0.8252 (ppp) cc_final: 0.7903 (ppp) REVERT: E 355 MET cc_start: 0.8125 (mtt) cc_final: 0.7849 (mtp) REVERT: F 47 MET cc_start: 0.6208 (mtm) cc_final: 0.5873 (mtp) outliers start: 31 outliers final: 14 residues processed: 223 average time/residue: 1.6139 time to fit residues: 393.9697 Evaluate side-chains 212 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN B 115 ASN D 225 ASN E 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17874 Z= 0.326 Angle : 0.603 11.877 24258 Z= 0.294 Chirality : 0.047 0.142 2700 Planarity : 0.005 0.036 3096 Dihedral : 7.007 101.768 2496 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.92 % Allowed : 13.73 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2190 helix: 0.80 (0.18), residues: 900 sheet: 0.68 (0.26), residues: 390 loop : 0.74 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE F 127 TYR 0.012 0.001 TYR C 188 ARG 0.005 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 2.078 Fit side-chains REVERT: A 328 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7383 (mtpp) REVERT: A 364 GLU cc_start: 0.7974 (pp20) cc_final: 0.7604 (tm-30) REVERT: B 25 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7078 (p0) REVERT: B 51 ASP cc_start: 0.7764 (p0) cc_final: 0.7561 (p0) REVERT: B 57 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: B 72 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: B 132 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8122 (ptm) REVERT: B 276 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: C 72 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: C 123 MET cc_start: 0.8824 (mmt) cc_final: 0.8449 (mmt) REVERT: C 372 ARG cc_start: 0.8515 (ptp-170) cc_final: 0.8141 (ptp-170) REVERT: D 72 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: D 80 ASP cc_start: 0.8007 (m-30) cc_final: 0.7614 (m-30) REVERT: D 153 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8677 (tp) REVERT: E 132 MET cc_start: 0.8327 (ppp) cc_final: 0.7993 (ppp) REVERT: E 222 ASP cc_start: 0.8361 (t70) cc_final: 0.8046 (t70) REVERT: E 355 MET cc_start: 0.8091 (mtt) cc_final: 0.7802 (mtp) REVERT: F 47 MET cc_start: 0.6191 (mtm) cc_final: 0.5862 (mtp) REVERT: F 349 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7865 (mp) REVERT: F 372 ARG cc_start: 0.7882 (ptt-90) cc_final: 0.7641 (ptt-90) outliers start: 36 outliers final: 19 residues processed: 218 average time/residue: 1.6213 time to fit residues: 387.7143 Evaluate side-chains 217 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 0.3980 chunk 204 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 180 optimal weight: 0.0270 chunk 188 optimal weight: 0.0170 chunk 198 optimal weight: 1.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17874 Z= 0.139 Angle : 0.526 10.723 24258 Z= 0.254 Chirality : 0.043 0.135 2700 Planarity : 0.004 0.035 3096 Dihedral : 6.526 98.684 2496 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.50 % Allowed : 14.21 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 2190 helix: 1.14 (0.18), residues: 900 sheet: 0.76 (0.26), residues: 390 loop : 0.87 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE C 255 TYR 0.009 0.001 TYR D 69 ARG 0.007 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 2.091 Fit side-chains REVERT: A 328 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7553 (mtpp) REVERT: A 364 GLU cc_start: 0.7938 (pp20) cc_final: 0.7680 (tm-30) REVERT: B 25 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7094 (p0) REVERT: B 132 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7991 (ptm) REVERT: B 176 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8726 (mmm) REVERT: B 276 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: C 123 MET cc_start: 0.8784 (mmt) cc_final: 0.8449 (mmt) REVERT: C 372 ARG cc_start: 0.8488 (ptp-170) cc_final: 0.8113 (ptp-170) REVERT: D 72 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: D 80 ASP cc_start: 0.7969 (m-30) cc_final: 0.7586 (m-30) REVERT: D 153 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8609 (tp) REVERT: E 132 MET cc_start: 0.8273 (ppp) cc_final: 0.7999 (ppp) REVERT: E 355 MET cc_start: 0.8094 (mtt) cc_final: 0.7831 (mtp) REVERT: F 47 MET cc_start: 0.6000 (mtm) cc_final: 0.5776 (mtp) REVERT: F 372 ARG cc_start: 0.7868 (ptt-90) cc_final: 0.7645 (ptt-90) outliers start: 28 outliers final: 13 residues processed: 217 average time/residue: 1.5957 time to fit residues: 379.9909 Evaluate side-chains 216 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN C 353 GLN D 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17874 Z= 0.280 Angle : 0.581 11.300 24258 Z= 0.282 Chirality : 0.046 0.137 2700 Planarity : 0.004 0.038 3096 Dihedral : 6.777 100.545 2496 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.39 % Allowed : 14.37 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2190 helix: 1.01 (0.18), residues: 900 sheet: 0.73 (0.26), residues: 390 loop : 0.83 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.008 0.001 PHE F 127 TYR 0.011 0.001 TYR C 188 ARG 0.007 0.000 ARG E 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 2.043 Fit side-chains REVERT: A 328 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7320 (mtpp) REVERT: A 364 GLU cc_start: 0.7908 (pp20) cc_final: 0.7652 (tm-30) REVERT: B 25 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.7069 (p0) REVERT: B 132 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8114 (ptm) REVERT: B 276 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7453 (mt-10) REVERT: C 123 MET cc_start: 0.8823 (mmt) cc_final: 0.8462 (mmt) REVERT: C 372 ARG cc_start: 0.8497 (ptp-170) cc_final: 0.8117 (ptp-170) REVERT: D 72 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: D 80 ASP cc_start: 0.7991 (m-30) cc_final: 0.7603 (m-30) REVERT: D 153 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8659 (tp) REVERT: D 328 LYS cc_start: 0.8810 (mttm) cc_final: 0.8602 (mttt) REVERT: E 132 MET cc_start: 0.8329 (ppp) cc_final: 0.8062 (ppp) REVERT: E 222 ASP cc_start: 0.8354 (t70) cc_final: 0.8029 (t70) REVERT: E 355 MET cc_start: 0.8125 (mtt) cc_final: 0.7854 (mtp) REVERT: F 190 MET cc_start: 0.8004 (ttt) cc_final: 0.7575 (ttm) REVERT: F 372 ARG cc_start: 0.7877 (ptt-90) cc_final: 0.7652 (ptt-90) outliers start: 26 outliers final: 16 residues processed: 212 average time/residue: 1.5893 time to fit residues: 370.0400 Evaluate side-chains 216 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 358 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 225 ASN E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.105155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.087297 restraints weight = 20870.917| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.30 r_work: 0.2809 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17874 Z= 0.249 Angle : 0.572 11.018 24258 Z= 0.278 Chirality : 0.046 0.138 2700 Planarity : 0.004 0.038 3096 Dihedral : 6.800 100.684 2496 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.44 % Allowed : 14.48 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.18), residues: 2190 helix: 0.98 (0.18), residues: 900 sheet: 0.69 (0.26), residues: 390 loop : 0.83 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.008 0.001 PHE F 127 TYR 0.009 0.001 TYR D 69 ARG 0.007 0.000 ARG E 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6654.26 seconds wall clock time: 117 minutes 13.20 seconds (7033.20 seconds total)