Starting phenix.real_space_refine on Sun Dec 29 13:55:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c4e_16425/12_2024/8c4e_16425_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c4e_16425/12_2024/8c4e_16425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c4e_16425/12_2024/8c4e_16425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c4e_16425/12_2024/8c4e_16425.map" model { file = "/net/cci-nas-00/data/ceres_data/8c4e_16425/12_2024/8c4e_16425_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c4e_16425/12_2024/8c4e_16425_trim.cif" } resolution = 2.6 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= 0.001 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 188 5.16 5 C 18152 2.51 5 N 4896 2.21 5 O 5528 1.98 5 H 28376 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 57172 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} 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: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: "H" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5760 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 349} 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: "K" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "L" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "M" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "N" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2707 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 22.77, per 1000 atoms: 0.40 Number of scatterers: 57172 At special positions: 0 Unit cell: (117.292, 97.468, 276.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 188 16.00 P 24 15.00 Mg 8 11.99 O 5528 8.00 N 4896 7.00 C 18152 6.00 H 28376 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.55 Conformation dependent library (CDL) restraints added in 3.6 seconds 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6760 Finding SS restraints... Secondary structure from input PDB file: 213 helices and 47 sheets defined 54.0% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.935A 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 171 through 175 Processing helix chain 'A' and resid 184 through 197 removed outlier: 3.538A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 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 282 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 332 through 336 removed outlier: 4.595A pdb=" N LYS A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.120A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.565A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.074A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix removed outlier: 4.657A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 285 through 288 removed outlier: 5.709A pdb=" N ASP B 288 " --> pdb=" O CYS B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 285 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 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.089A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.934A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.028A 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 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 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 353 removed outlier: 3.562A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 353' Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.917A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.964A 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 removed outlier: 3.756A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 263 Proline residue: D 258 - end of helix removed outlier: 4.751A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 284 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 337 through 349 Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.876A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.873A 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 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 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 337 through 349 Processing helix chain 'E' and resid 350 through 353 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.753A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.868A 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: 3.533A pdb=" N LYS F 215 " --> pdb=" O ASP F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 263 Proline residue: F 258 - end of helix removed outlier: 4.658A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.171A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 3.801A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.048A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.784A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 260 Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 261 through 262 No H-bonds generated for 'chain 'G' and resid 261 through 262' Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 295 Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 337 through 349 Processing helix chain 'G' and resid 350 through 353 Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing helix chain 'H' and resid 55 through 61 Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.922A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.776A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 260 Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 261 through 262 No H-bonds generated for 'chain 'H' and resid 261 through 262' Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 295 removed outlier: 4.202A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.899A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 368 through 374 removed outlier: 3.999A pdb=" N ARG H 372 " --> pdb=" O SER H 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 529 removed outlier: 3.531A pdb=" N VAL K 529 " --> pdb=" O LEU K 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 531 through 536 Processing helix chain 'K' and resid 541 through 554 Processing helix chain 'K' and resid 561 through 576 Processing helix chain 'K' and resid 579 through 591 removed outlier: 3.601A pdb=" N GLN K 589 " --> pdb=" O ALA K 585 " (cutoff:3.500A) Processing helix chain 'K' and resid 592 through 595 removed outlier: 3.685A pdb=" N LYS K 595 " --> pdb=" O ASP K 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 592 through 595' Processing helix chain 'K' and resid 596 through 612 Processing helix chain 'K' and resid 615 through 631 Processing helix chain 'K' and resid 635 through 639 Processing helix chain 'K' and resid 640 through 651 Processing helix chain 'K' and resid 654 through 658 Processing helix chain 'K' and resid 678 through 682 Processing helix chain 'L' and resid 523 through 529 removed outlier: 3.995A pdb=" N SER L 527 " --> pdb=" O SER L 524 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 531 through 536 removed outlier: 3.576A pdb=" N HIS L 536 " --> pdb=" O VAL L 532 " (cutoff:3.500A) Processing helix chain 'L' and resid 541 through 554 Processing helix chain 'L' and resid 561 through 576 Processing helix chain 'L' and resid 579 through 591 Processing helix chain 'L' and resid 592 through 595 Processing helix chain 'L' and resid 596 through 612 Processing helix chain 'L' and resid 615 through 631 Processing helix chain 'L' and resid 635 through 639 Processing helix chain 'L' and resid 640 through 651 Processing helix chain 'L' and resid 654 through 658 Processing helix chain 'L' and resid 676 through 682 removed outlier: 3.698A pdb=" N LEU L 681 " --> pdb=" O THR L 677 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS L 682 " --> pdb=" O VAL L 678 " (cutoff:3.500A) Processing helix chain 'M' and resid 525 through 529 Processing helix chain 'M' and resid 531 through 536 Processing helix chain 'M' and resid 541 through 554 Processing helix chain 'M' and resid 561 through 576 Processing helix chain 'M' and resid 579 through 590 Processing helix chain 'M' and resid 592 through 595 Processing helix chain 'M' and resid 596 through 612 Processing helix chain 'M' and resid 615 through 631 Processing helix chain 'M' and resid 635 through 639 Processing helix chain 'M' and resid 640 through 651 Processing helix chain 'M' and resid 654 through 658 Processing helix chain 'N' and resid 525 through 529 Processing helix chain 'N' and resid 531 through 536 Processing helix chain 'N' and resid 541 through 554 Processing helix chain 'N' and resid 561 through 576 Processing helix chain 'N' and resid 579 through 590 Processing helix chain 'N' and resid 591 through 595 removed outlier: 5.920A pdb=" N ASP N 594 " --> pdb=" O SER N 591 " (cutoff:3.500A) Processing helix chain 'N' and resid 596 through 612 Processing helix chain 'N' and resid 615 through 631 Processing helix chain 'N' and resid 635 through 639 Processing helix chain 'N' and resid 640 through 651 Processing helix chain 'N' and resid 654 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 107 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.576A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.330A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB3, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.296A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.394A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.573A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC3, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.445A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.585A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.396A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.694A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.392A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD9, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.668A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AE2, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AE4, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.432A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AE6, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.560A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AE8, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AE9, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AF1, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.427A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 238 through 241 1480 hydrogen bonds defined for protein. 3849 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: 24.58 Time building geometry restraints manager: 14.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28268 1.03 - 1.23: 236 1.23 - 1.42: 11941 1.42 - 1.62: 17011 1.62 - 1.81: 332 Bond restraints: 57788 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" HE1 HIC F 73 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" CE1 HIC D 73 " pdb=" HE1 HIC D 73 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" CE1 HIC G 73 " pdb=" HE1 HIC G 73 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" CE1 HIC E 73 " pdb=" HE1 HIC E 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.80e+01 bond pdb=" CE1 HIC H 73 " pdb=" HE1 HIC H 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.77e+01 ... (remaining 57783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 103046 1.73 - 3.46: 1226 3.46 - 5.18: 214 5.18 - 6.91: 35 6.91 - 8.64: 7 Bond angle restraints: 104528 Sorted by residual: angle pdb=" N ILE A 282 " pdb=" CA ILE A 282 " pdb=" C ILE A 282 " ideal model delta sigma weight residual 110.21 104.07 6.14 1.13e+00 7.83e-01 2.95e+01 angle pdb=" C GLY B 42 " pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 121.70 130.34 -8.64 1.80e+00 3.09e-01 2.30e+01 angle pdb=" C GLY G 42 " pdb=" N VAL G 43 " pdb=" CA VAL G 43 " ideal model delta sigma weight residual 121.70 129.52 -7.82 1.80e+00 3.09e-01 1.89e+01 angle pdb=" C GLY C 42 " pdb=" N VAL C 43 " pdb=" CA VAL C 43 " ideal model delta sigma weight residual 121.70 129.36 -7.66 1.80e+00 3.09e-01 1.81e+01 angle pdb=" C GLY D 42 " pdb=" N VAL D 43 " pdb=" CA VAL D 43 " ideal model delta sigma weight residual 121.70 129.22 -7.52 1.80e+00 3.09e-01 1.74e+01 ... (remaining 104523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 25947 31.05 - 62.09: 1148 62.09 - 93.14: 93 93.14 - 124.18: 17 124.18 - 155.23: 11 Dihedral angle restraints: 27216 sinusoidal: 14996 harmonic: 12220 Sorted by residual: dihedral pdb=" CA VAL A 9 " pdb=" C VAL A 9 " pdb=" N CYS A 10 " pdb=" CA CYS A 10 " ideal model delta harmonic sigma weight residual -180.00 -145.81 -34.19 0 5.00e+00 4.00e-02 4.68e+01 dihedral pdb=" O2A ADP E 802 " pdb=" O3A ADP E 802 " pdb=" PA ADP E 802 " pdb=" PB ADP E 802 " ideal model delta sinusoidal sigma weight residual -60.00 95.23 -155.23 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP H 803 " pdb=" O3A ADP H 803 " pdb=" PA ADP H 803 " pdb=" PB ADP H 803 " ideal model delta sinusoidal sigma weight residual -60.00 94.38 -154.38 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 27213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2888 0.036 - 0.072: 1101 0.072 - 0.108: 331 0.108 - 0.144: 103 0.144 - 0.180: 5 Chirality restraints: 4428 Sorted by residual: chirality pdb=" CB ILE A 76 " pdb=" CA ILE A 76 " pdb=" CG1 ILE A 76 " pdb=" CG2 ILE A 76 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA ILE A 282 " pdb=" N ILE A 282 " pdb=" C ILE A 282 " pdb=" CB ILE A 282 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 4425 not shown) Planarity restraints: 8552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 28 " 0.157 9.50e-02 1.11e+02 5.26e-02 3.51e+00 pdb=" NE ARG F 28 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG F 28 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG F 28 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 28 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG F 28 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG F 28 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG F 28 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG F 28 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 12 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C ASN H 12 " 0.026 2.00e-02 2.50e+03 pdb=" O ASN H 12 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY H 13 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 128 " 0.005 2.00e-02 2.50e+03 1.15e-02 1.99e+00 pdb=" CG ASN E 128 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN E 128 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 128 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN E 128 " 0.005 2.00e-02 2.50e+03 pdb="HD22 ASN E 128 " -0.001 2.00e-02 2.50e+03 ... (remaining 8549 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 1070 2.06 - 2.70: 93061 2.70 - 3.33: 177143 3.33 - 3.97: 235776 3.97 - 4.60: 364556 Nonbonded interactions: 871606 Sorted by model distance: nonbonded pdb=" HZ2 LYS C 213 " pdb=" O2' ADP C 401 " model vdw 1.431 2.450 nonbonded pdb=" HZ1 LYS E 213 " pdb=" O2' ADP E 802 " model vdw 1.459 2.450 nonbonded pdb=" HZ2 LYS B 213 " pdb=" O2' ADP B 402 " model vdw 1.508 2.450 nonbonded pdb=" O GLY A 168 " pdb=" H VAL C 43 " model vdw 1.542 2.450 nonbonded pdb=" O ASP L 557 " pdb=" HG1 THR L 560 " model vdw 1.542 2.450 ... (remaining 871601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 375) selection = (chain 'B' and resid 6 through 375) selection = (chain 'C' and resid 6 through 375) selection = (chain 'D' and resid 6 through 375) selection = (chain 'E' and resid 6 through 375) selection = (chain 'F' and resid 6 through 375) selection = (chain 'G' and resid 6 through 375) selection = (chain 'H' and resid 6 through 375) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 6.540 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: 0.770 Extract box with map and model: 1.640 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 100.070 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.270 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:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.005 0.060 29412 Z= 0.298 Angle : 0.657 8.641 39884 Z= 0.345 Chirality : 0.043 0.180 4428 Planarity : 0.004 0.069 5104 Dihedral : 16.878 155.228 10968 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.47 % Favored : 97.39 % Rotamer: Outliers : 1.13 % Allowed : 11.35 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.56 (0.14), residues: 3600 helix: 0.27 (0.13), residues: 1554 sheet: -0.15 (0.29), residues: 320 loop : 0.83 (0.16), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.005 0.001 HIS F 161 PHE 0.020 0.002 PHE B 266 TYR 0.017 0.001 TYR E 143 ARG 0.010 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7807 (mp) REVERT: E 269 MET cc_start: 0.8696 (mtp) cc_final: 0.8429 (mtt) REVERT: H 132 MET cc_start: 0.8183 (tmt) cc_final: 0.7963 (OUTLIER) outliers start: 35 outliers final: 30 residues processed: 333 average time/residue: 2.5718 time to fit residues: 1005.1878 Evaluate side-chains 335 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 305 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 516 SER Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 110 optimal weight: 0.0970 chunk 173 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 330 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN E 128 ASN E 162 ASN M 625 GLN ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29412 Z= 0.251 Angle : 0.650 8.201 39884 Z= 0.333 Chirality : 0.046 0.213 4428 Planarity : 0.005 0.070 5104 Dihedral : 11.553 156.000 4116 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 2.01 % Allowed : 10.73 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.64 (0.14), residues: 3600 helix: 0.41 (0.13), residues: 1569 sheet: -0.46 (0.27), residues: 360 loop : 0.91 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.006 0.001 HIS F 161 PHE 0.017 0.002 PHE K 568 TYR 0.014 0.001 TYR E 143 ARG 0.006 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 316 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 GLU cc_start: 0.7800 (pm20) cc_final: 0.7565 (pm20) REVERT: C 105 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7810 (mp) REVERT: E 269 MET cc_start: 0.8716 (mtp) cc_final: 0.8436 (mtt) REVERT: H 113 LYS cc_start: 0.6193 (OUTLIER) cc_final: 0.4757 (mptt) REVERT: L 595 LYS cc_start: 0.6703 (ptpt) cc_final: 0.6345 (pttm) REVERT: N 679 ASP cc_start: 0.6622 (m-30) cc_final: 0.6335 (m-30) outliers start: 62 outliers final: 36 residues processed: 357 average time/residue: 2.6849 time to fit residues: 1120.1376 Evaluate side-chains 327 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 331 optimal weight: 0.7980 chunk 357 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 328 optimal weight: 0.0270 chunk 112 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN M 612 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29412 Z= 0.207 Angle : 0.607 8.034 39884 Z= 0.305 Chirality : 0.044 0.192 4428 Planarity : 0.004 0.046 5104 Dihedral : 11.184 159.612 4097 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.91 % Allowed : 11.06 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.71 (0.14), residues: 3600 helix: 0.51 (0.13), residues: 1569 sheet: -0.27 (0.29), residues: 320 loop : 0.84 (0.16), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 79 HIS 0.005 0.001 HIS F 161 PHE 0.015 0.001 PHE A 31 TYR 0.014 0.001 TYR E 143 ARG 0.006 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 314 time to evaluate : 3.498 Fit side-chains revert: symmetry clash REVERT: A 364 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6006 (mp0) REVERT: C 105 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7746 (mp) REVERT: D 191 LYS cc_start: 0.8783 (ttpp) cc_final: 0.8438 (ttmt) REVERT: E 269 MET cc_start: 0.8709 (mtp) cc_final: 0.8443 (mtt) REVERT: H 113 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.4722 (mptt) REVERT: L 595 LYS cc_start: 0.6740 (ptpt) cc_final: 0.6407 (pttm) REVERT: N 666 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7445 (pt) REVERT: N 679 ASP cc_start: 0.6563 (m-30) cc_final: 0.6288 (m-30) outliers start: 59 outliers final: 34 residues processed: 352 average time/residue: 2.6357 time to fit residues: 1086.6379 Evaluate side-chains 329 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 291 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 604 GLU Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 158 optimal weight: 0.0870 chunk 222 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 314 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 128 ASN G 121 GLN H 246 GLN H 360 GLN K 645 ASN M 612 HIS ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29412 Z= 0.286 Angle : 0.636 8.463 39884 Z= 0.322 Chirality : 0.046 0.215 4428 Planarity : 0.005 0.051 5104 Dihedral : 11.148 157.088 4089 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 2.30 % Allowed : 11.02 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3600 helix: 0.49 (0.13), residues: 1569 sheet: -0.39 (0.26), residues: 360 loop : 0.85 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 PHE 0.019 0.002 PHE B 266 TYR 0.013 0.001 TYR E 143 ARG 0.007 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 301 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6084 (mp0) REVERT: C 105 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7798 (mp) REVERT: D 191 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8404 (ttmm) REVERT: G 147 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7892 (ptp-110) REVERT: H 113 LYS cc_start: 0.6123 (OUTLIER) cc_final: 0.4755 (mptt) REVERT: L 595 LYS cc_start: 0.6753 (ptpt) cc_final: 0.6425 (pttm) REVERT: N 666 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7486 (pt) REVERT: N 679 ASP cc_start: 0.6627 (m-30) cc_final: 0.6338 (m-30) outliers start: 71 outliers final: 46 residues processed: 353 average time/residue: 2.6632 time to fit residues: 1108.7614 Evaluate side-chains 348 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 544 GLU Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 261 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 300 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 128 ASN M 612 HIS ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29412 Z= 0.241 Angle : 0.616 8.305 39884 Z= 0.310 Chirality : 0.045 0.209 4428 Planarity : 0.005 0.063 5104 Dihedral : 11.117 175.712 4089 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 2.08 % Allowed : 11.35 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.72 (0.14), residues: 3600 helix: 0.54 (0.13), residues: 1570 sheet: -0.37 (0.26), residues: 360 loop : 0.87 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 340 HIS 0.005 0.001 HIS F 161 PHE 0.016 0.001 PHE A 31 TYR 0.013 0.001 TYR E 143 ARG 0.008 0.000 ARG G 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6147 (mp0) REVERT: C 105 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7955 (mp) REVERT: C 167 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: D 191 LYS cc_start: 0.8783 (ttpp) cc_final: 0.8446 (ttmt) REVERT: H 113 LYS cc_start: 0.6128 (OUTLIER) cc_final: 0.4765 (mptt) REVERT: L 595 LYS cc_start: 0.6715 (ptpt) cc_final: 0.6494 (pttm) REVERT: L 657 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7060 (ttm110) REVERT: N 666 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7455 (pt) REVERT: N 679 ASP cc_start: 0.6629 (m-30) cc_final: 0.6331 (m-30) outliers start: 64 outliers final: 45 residues processed: 352 average time/residue: 2.6085 time to fit residues: 1077.0397 Evaluate side-chains 344 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 128 ASN H 360 GLN M 612 HIS ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29412 Z= 0.312 Angle : 0.648 8.501 39884 Z= 0.328 Chirality : 0.046 0.225 4428 Planarity : 0.005 0.062 5104 Dihedral : 11.189 171.555 4089 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.14 % Rotamer: Outliers : 2.50 % Allowed : 11.12 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.14), residues: 3600 helix: 0.49 (0.13), residues: 1570 sheet: -0.41 (0.26), residues: 360 loop : 0.86 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 340 HIS 0.006 0.001 HIS F 161 PHE 0.020 0.002 PHE B 266 TYR 0.012 0.002 TYR E 143 ARG 0.007 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 300 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6161 (mp0) REVERT: C 105 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7852 (mp) REVERT: C 167 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: D 191 LYS cc_start: 0.8821 (ttpp) cc_final: 0.8452 (ttmt) REVERT: G 147 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7886 (ptp-110) REVERT: H 113 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.4723 (mptt) REVERT: L 595 LYS cc_start: 0.6777 (ptpt) cc_final: 0.6563 (pttm) REVERT: L 608 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: L 657 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7076 (ttm110) REVERT: N 666 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7498 (pt) REVERT: N 679 ASP cc_start: 0.6682 (m-30) cc_final: 0.6373 (m-30) outliers start: 77 outliers final: 48 residues processed: 356 average time/residue: 2.6140 time to fit residues: 1093.7313 Evaluate side-chains 353 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 4.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain L residue 608 GLU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 590 CYS Chi-restraints excluded: chain N residue 666 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 296 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 350 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN H 360 GLN M 612 HIS M 625 GLN ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29412 Z= 0.223 Angle : 0.611 8.263 39884 Z= 0.307 Chirality : 0.044 0.208 4428 Planarity : 0.005 0.066 5104 Dihedral : 11.009 178.206 4089 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 2.11 % Allowed : 11.67 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.77 (0.14), residues: 3600 helix: 0.60 (0.13), residues: 1576 sheet: -0.36 (0.28), residues: 320 loop : 0.86 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.005 0.001 HIS F 161 PHE 0.016 0.001 PHE A 31 TYR 0.013 0.001 TYR E 143 ARG 0.009 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.8639 (mpp) cc_final: 0.6818 (mpt) REVERT: A 364 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: C 105 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7928 (mp) REVERT: C 167 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: D 191 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8440 (ttmt) REVERT: G 147 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7851 (ptp-110) REVERT: H 113 LYS cc_start: 0.6071 (OUTLIER) cc_final: 0.4694 (mptt) REVERT: L 595 LYS cc_start: 0.6736 (ptpt) cc_final: 0.6519 (pttm) REVERT: L 599 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6719 (tt) REVERT: L 657 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7045 (ttm110) REVERT: N 679 ASP cc_start: 0.6671 (m-30) cc_final: 0.6358 (m-30) outliers start: 65 outliers final: 46 residues processed: 357 average time/residue: 2.6738 time to fit residues: 1134.5750 Evaluate side-chains 353 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 590 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.2980 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 173 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 128 ASN M 612 HIS M 625 GLN ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29412 Z= 0.276 Angle : 0.629 8.325 39884 Z= 0.317 Chirality : 0.045 0.220 4428 Planarity : 0.005 0.065 5104 Dihedral : 11.033 179.112 4089 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.22 % Rotamer: Outliers : 2.20 % Allowed : 11.74 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.74 (0.14), residues: 3600 helix: 0.57 (0.13), residues: 1576 sheet: -0.38 (0.26), residues: 360 loop : 0.87 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS F 161 PHE 0.017 0.002 PHE A 31 TYR 0.012 0.001 TYR E 143 ARG 0.010 0.001 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 304 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: C 105 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 167 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: D 191 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8458 (ttmt) REVERT: E 25 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7277 (t70) REVERT: F 372 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7772 (mtm-85) REVERT: G 147 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7878 (ptp-110) REVERT: H 113 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.4703 (mptt) REVERT: L 595 LYS cc_start: 0.6744 (ptpt) cc_final: 0.6525 (pttm) REVERT: L 599 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6701 (tt) REVERT: L 657 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7059 (ttm110) REVERT: N 679 ASP cc_start: 0.6697 (m-30) cc_final: 0.6382 (m-30) outliers start: 68 outliers final: 48 residues processed: 354 average time/residue: 2.6003 time to fit residues: 1082.8916 Evaluate side-chains 355 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 590 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 326 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 295 optimal weight: 0.0670 chunk 309 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN M 612 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29412 Z= 0.250 Angle : 0.620 8.324 39884 Z= 0.312 Chirality : 0.045 0.216 4428 Planarity : 0.005 0.071 5104 Dihedral : 10.955 178.353 4089 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.11 % Rotamer: Outliers : 2.20 % Allowed : 11.84 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.76 (0.14), residues: 3600 helix: 0.60 (0.13), residues: 1576 sheet: -0.38 (0.26), residues: 360 loop : 0.88 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.005 0.001 HIS F 161 PHE 0.017 0.001 PHE B 266 TYR 0.013 0.001 TYR E 143 ARG 0.011 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 309 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 GLN cc_start: 0.7403 (tp40) cc_final: 0.6906 (tp-100) REVERT: A 364 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: C 105 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7962 (mp) REVERT: C 167 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: D 191 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8453 (ttmt) REVERT: E 25 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7279 (t70) REVERT: E 178 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8087 (mp) REVERT: F 372 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7756 (mtm-85) REVERT: G 147 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7860 (ptp-110) REVERT: H 113 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.4722 (mptt) REVERT: L 595 LYS cc_start: 0.6745 (ptpt) cc_final: 0.6527 (pttm) REVERT: L 599 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6697 (tt) REVERT: L 657 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7050 (ttm110) REVERT: N 679 ASP cc_start: 0.6684 (m-30) cc_final: 0.6367 (m-30) outliers start: 68 outliers final: 47 residues processed: 359 average time/residue: 2.6664 time to fit residues: 1126.4549 Evaluate side-chains 363 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 541 ASP Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 590 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 2.9990 chunk 345 optimal weight: 0.0670 chunk 211 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 362 optimal weight: 4.9990 chunk 333 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 128 ASN M 612 HIS ** N 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29412 Z= 0.273 Angle : 0.632 8.386 39884 Z= 0.319 Chirality : 0.045 0.222 4428 Planarity : 0.005 0.071 5104 Dihedral : 10.969 179.361 4089 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.75 % Favored : 97.17 % Rotamer: Outliers : 1.98 % Allowed : 12.22 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.73 (0.14), residues: 3600 helix: 0.58 (0.13), residues: 1576 sheet: -0.39 (0.26), residues: 360 loop : 0.86 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.006 0.001 HIS F 161 PHE 0.017 0.002 PHE A 31 TYR 0.012 0.001 TYR E 143 ARG 0.010 0.001 ARG F 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7200 Ramachandran restraints generated. 3600 Oldfield, 0 Emsley, 3600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 305 time to evaluate : 4.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 GLN cc_start: 0.7392 (tp40) cc_final: 0.6889 (tp-100) REVERT: A 364 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: C 105 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7967 (mp) REVERT: C 167 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: D 191 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8452 (ttmt) REVERT: E 25 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7281 (t70) REVERT: E 178 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8087 (mp) REVERT: F 372 ARG cc_start: 0.7963 (mtp180) cc_final: 0.7756 (mtm-85) REVERT: G 147 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7869 (ptp-110) REVERT: H 113 LYS cc_start: 0.6157 (OUTLIER) cc_final: 0.4681 (mptt) REVERT: L 595 LYS cc_start: 0.6750 (ptpt) cc_final: 0.6531 (pttm) REVERT: L 599 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6652 (tt) REVERT: L 657 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7059 (ttm110) REVERT: N 679 ASP cc_start: 0.6706 (m-30) cc_final: 0.6397 (m-30) outliers start: 61 outliers final: 47 residues processed: 349 average time/residue: 2.6470 time to fit residues: 1084.3250 Evaluate side-chains 358 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 360 GLN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 147 ARG Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 291 LYS Chi-restraints excluded: chain L residue 527 SER Chi-restraints excluded: chain L residue 589 GLN Chi-restraints excluded: chain L residue 599 LEU Chi-restraints excluded: chain L residue 657 ARG Chi-restraints excluded: chain M residue 544 GLU Chi-restraints excluded: chain M residue 569 ASP Chi-restraints excluded: chain M residue 651 ILE Chi-restraints excluded: chain M residue 682 HIS Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 566 ARG Chi-restraints excluded: chain N residue 590 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 289 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.092794 restraints weight = 102013.176| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.03 r_work: 0.2938 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29412 Z= 0.241 Angle : 0.618 8.281 39884 Z= 0.310 Chirality : 0.045 0.215 4428 Planarity : 0.005 0.073 5104 Dihedral : 10.855 177.455 4089 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.81 % Favored : 97.11 % Rotamer: Outliers : 1.95 % Allowed : 12.29 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.78 (0.14), residues: 3600 helix: 0.63 (0.13), residues: 1576 sheet: -0.38 (0.26), residues: 360 loop : 0.87 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.006 0.001 HIS F 161 PHE 0.016 0.001 PHE A 31 TYR 0.013 0.001 TYR E 143 ARG 0.011 0.000 ARG F 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16387.65 seconds wall clock time: 281 minutes 23.43 seconds (16883.43 seconds total)