Starting phenix.real_space_refine on Sun Mar 17 20:29:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/03_2024/6ap1_8887_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/03_2024/6ap1_8887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/03_2024/6ap1_8887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/03_2024/6ap1_8887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/03_2024/6ap1_8887_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/03_2024/6ap1_8887_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 54 5.16 5 Be 3 3.05 5 C 11831 2.51 5 N 3185 2.21 5 O 3742 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 398": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "F GLU 332": "OE1" <-> "OE2" Residue "H GLU 311": "OE1" <-> "OE2" Residue "I GLU 311": "OE1" <-> "OE2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "K GLU 311": "OE1" <-> "OE2" Residue "L GLU 311": "OE1" <-> "OE2" Residue "M GLU 311": "OE1" <-> "OE2" Residue "N GLU 311": "OE1" <-> "OE2" Residue "O GLU 311": "OE1" <-> "OE2" Residue "P GLU 311": "OE1" <-> "OE2" Residue "Q GLU 311": "OE1" <-> "OE2" Residue "R GLU 311": "OE1" <-> "OE2" Residue "S GLU 311": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18838 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2427 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "E" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2360 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 68 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 10, 68 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 8, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 7} Chain: "F" Number of atoms: 2387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2387 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain breaks: 1 Chain: "H" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "J" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "K" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "L" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "M" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "N" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "O" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "P" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "R" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "S" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.05, per 1000 atoms: 0.53 Number of scatterers: 18838 At special positions: 0 Unit cell: (156.742, 103.033, 157.838, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 54 16.00 P 10 15.00 Mg 4 11.99 F 9 9.00 O 3742 8.00 N 3185 7.00 C 11831 6.00 Be 3 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.19 Conformation dependent library (CDL) restraints added in 3.5 seconds 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 17 sheets defined 53.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 139 through 154 removed outlier: 5.329A pdb=" N LEU A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 209 through 223 removed outlier: 5.317A pdb=" N VAL A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 246 through 261 removed outlier: 3.539A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 336 through 355 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 421 through 432 Processing helix chain 'B' and resid 113 through 121 removed outlier: 5.048A pdb=" N SER B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 154 removed outlier: 5.329A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Proline residue: B 152 - end of helix Processing helix chain 'B' and resid 179 through 189 Processing helix chain 'B' and resid 209 through 223 removed outlier: 4.505A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 336 through 355 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 404 through 412 Processing helix chain 'B' and resid 421 through 432 Processing helix chain 'C' and resid 113 through 121 removed outlier: 5.048A pdb=" N SER C 121 " --> pdb=" O GLY C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 139 through 154 removed outlier: 5.330A pdb=" N LEU C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'C' and resid 336 through 355 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 421 through 432 Processing helix chain 'D' and resid 113 through 121 removed outlier: 5.048A pdb=" N SER D 121 " --> pdb=" O GLY D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 154 removed outlier: 5.329A pdb=" N LEU D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 179 through 189 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 336 through 355 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 404 through 412 Processing helix chain 'D' and resid 421 through 432 Processing helix chain 'E' and resid 139 through 153 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'E' and resid 212 through 222 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 246 through 260 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 321 through 330 Processing helix chain 'E' and resid 336 through 355 Proline residue: E 350 - end of helix Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 421 through 432 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 139 through 154 removed outlier: 4.435A pdb=" N LEU F 151 " --> pdb=" O GLU F 147 " (cutoff:3.500A) Proline residue: F 152 - end of helix Processing helix chain 'F' and resid 156 through 159 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 207 through 224 removed outlier: 4.800A pdb=" N GLU F 211 " --> pdb=" O GLY F 208 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 217 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 265 removed outlier: 4.162A pdb=" N LEU F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 258 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL F 263 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLY F 264 " --> pdb=" O MET F 260 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN F 265 " --> pdb=" O ASN F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.578A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 321 through 331 Processing helix chain 'F' and resid 336 through 355 removed outlier: 4.013A pdb=" N MET F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Proline residue: F 350 - end of helix Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 403 through 412 removed outlier: 3.510A pdb=" N LEU F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 432 Processing helix chain 'H' and resid 293 through 310 removed outlier: 4.030A pdb=" N GLN H 298 " --> pdb=" O ILE H 294 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR H 310 " --> pdb=" O SER H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 329 removed outlier: 3.838A pdb=" N THR H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 324 " --> pdb=" O LEU H 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 310 removed outlier: 4.544A pdb=" N TYR I 310 " --> pdb=" O SER I 306 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 329 removed outlier: 3.837A pdb=" N THR I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU I 324 " --> pdb=" O LEU I 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 310 removed outlier: 4.029A pdb=" N GLN J 298 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR J 310 " --> pdb=" O SER J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU J 324 " --> pdb=" O LEU J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 310 removed outlier: 4.544A pdb=" N TYR K 310 " --> pdb=" O SER K 306 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU K 324 " --> pdb=" O LEU K 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 310 removed outlier: 4.030A pdb=" N GLN L 298 " --> pdb=" O ILE L 294 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR L 310 " --> pdb=" O SER L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 329 removed outlier: 3.840A pdb=" N THR L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU L 324 " --> pdb=" O LEU L 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 310 removed outlier: 4.544A pdb=" N TYR M 310 " --> pdb=" O SER M 306 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR M 321 " --> pdb=" O LYS M 317 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 324 " --> pdb=" O LEU M 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 310 removed outlier: 4.032A pdb=" N GLN N 298 " --> pdb=" O ILE N 294 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR N 310 " --> pdb=" O SER N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 329 removed outlier: 3.838A pdb=" N THR N 321 " --> pdb=" O LYS N 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU N 324 " --> pdb=" O LEU N 320 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 310 removed outlier: 4.544A pdb=" N TYR O 310 " --> pdb=" O SER O 306 " (cutoff:3.500A) Processing helix chain 'O' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR O 321 " --> pdb=" O LYS O 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU O 324 " --> pdb=" O LEU O 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 293 through 310 removed outlier: 4.030A pdb=" N GLN P 298 " --> pdb=" O ILE P 294 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR P 310 " --> pdb=" O SER P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 313 through 329 removed outlier: 3.840A pdb=" N THR P 321 " --> pdb=" O LYS P 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU P 324 " --> pdb=" O LEU P 320 " (cutoff:3.500A) Processing helix chain 'Q' and resid 290 through 310 removed outlier: 4.545A pdb=" N TYR Q 310 " --> pdb=" O SER Q 306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 313 through 329 removed outlier: 3.840A pdb=" N THR Q 321 " --> pdb=" O LYS Q 317 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU Q 324 " --> pdb=" O LEU Q 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 310 removed outlier: 4.030A pdb=" N GLN R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR R 310 " --> pdb=" O SER R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 329 removed outlier: 3.838A pdb=" N THR R 321 " --> pdb=" O LYS R 317 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU R 324 " --> pdb=" O LEU R 320 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 310 removed outlier: 4.546A pdb=" N TYR S 310 " --> pdb=" O SER S 306 " (cutoff:3.500A) Processing helix chain 'S' and resid 313 through 329 removed outlier: 3.839A pdb=" N THR S 321 " --> pdb=" O LYS S 317 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU S 324 " --> pdb=" O LEU S 320 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 170 through 173 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.083A pdb=" N LEU A 271 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 360 through 362 Processing sheet with id= D, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= E, first strand: chain 'B' and resid 193 through 197 removed outlier: 3.502A pdb=" N LEU B 271 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 231 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 360 through 362 Processing sheet with id= G, first strand: chain 'C' and resid 170 through 173 Processing sheet with id= H, first strand: chain 'C' and resid 227 through 231 removed outlier: 3.828A pdb=" N ILE C 231 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 360 through 362 Processing sheet with id= J, first strand: chain 'D' and resid 170 through 173 Processing sheet with id= K, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.973A pdb=" N ILE D 231 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 275 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 360 through 362 Processing sheet with id= M, first strand: chain 'E' and resid 170 through 173 Processing sheet with id= N, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= O, first strand: chain 'E' and resid 360 through 362 Processing sheet with id= P, first strand: chain 'F' and resid 124 through 126 removed outlier: 6.832A pdb=" N ARG F 292 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N TYR F 172 " --> pdb=" O ARG F 292 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE F 294 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 360 through 362 840 hydrogen bonds defined for protein. 2475 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: 4.67 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3400 1.31 - 1.44: 4401 1.44 - 1.56: 11159 1.56 - 1.69: 54 1.69 - 1.82: 96 Bond restraints: 19110 Sorted by residual: bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.351 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C5 ADP C 701 " pdb=" C6 ADP C 701 " ideal model delta sigma weight residual 1.490 1.356 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.359 0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.361 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C5 ADP B 701 " pdb=" C6 ADP B 701 " ideal model delta sigma weight residual 1.490 1.362 0.128 2.00e-02 2.50e+03 4.10e+01 ... (remaining 19105 not shown) Histogram of bond angle deviations from ideal: 93.79 - 102.53: 124 102.53 - 111.27: 7743 111.27 - 120.01: 9938 120.01 - 128.75: 7912 128.75 - 137.49: 108 Bond angle restraints: 25825 Sorted by residual: angle pdb=" O1B ADP B 701 " pdb=" PB ADP B 701 " pdb=" O3B ADP B 701 " ideal model delta sigma weight residual 119.90 94.35 25.55 3.00e+00 1.11e-01 7.25e+01 angle pdb=" C LEU F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.84 130.15 -10.31 1.25e+00 6.40e-01 6.81e+01 angle pdb=" C GLU D 398 " pdb=" N PRO D 399 " pdb=" CA PRO D 399 " ideal model delta sigma weight residual 119.84 129.97 -10.13 1.25e+00 6.40e-01 6.57e+01 angle pdb=" N GLY F 269 " pdb=" CA GLY F 269 " pdb=" C GLY F 269 " ideal model delta sigma weight residual 115.32 126.06 -10.74 1.38e+00 5.25e-01 6.05e+01 angle pdb=" O1B ADP A 701 " pdb=" PB ADP A 701 " pdb=" O3B ADP A 701 " ideal model delta sigma weight residual 119.90 96.89 23.01 3.00e+00 1.11e-01 5.88e+01 ... (remaining 25820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 11612 34.50 - 69.01: 198 69.01 - 103.51: 16 103.51 - 138.01: 2 138.01 - 172.52: 4 Dihedral angle restraints: 11832 sinusoidal: 4869 harmonic: 6963 Sorted by residual: dihedral pdb=" CA LYS B 205 " pdb=" C LYS B 205 " pdb=" N TRP B 206 " pdb=" CA TRP B 206 " ideal model delta harmonic sigma weight residual 180.00 -142.41 -37.59 0 5.00e+00 4.00e-02 5.65e+01 dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.51 -172.52 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA GLY A 269 " pdb=" C GLY A 269 " pdb=" N VAL A 270 " pdb=" CA VAL A 270 " ideal model delta harmonic sigma weight residual -180.00 -145.99 -34.01 0 5.00e+00 4.00e-02 4.63e+01 ... (remaining 11829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2312 0.110 - 0.221: 577 0.221 - 0.331: 87 0.331 - 0.441: 7 0.441 - 0.551: 1 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CA GLU F 147 " pdb=" N GLU F 147 " pdb=" C GLU F 147 " pdb=" CB GLU F 147 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" CA GLU F 139 " pdb=" N GLU F 139 " pdb=" C GLU F 139 " pdb=" CB GLU F 139 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ILE F 278 " pdb=" N ILE F 278 " pdb=" C ILE F 278 " pdb=" CB ILE F 278 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 2981 not shown) Planarity restraints: 3305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C AACE G 0 " -0.014 2.00e-02 2.50e+03 5.76e-02 4.14e+01 pdb=" O AACE G 0 " -0.015 2.00e-02 2.50e+03 pdb=" CH3AACE G 0 " 0.051 2.00e-02 2.50e+03 pdb=" N ASP G 165 " -0.093 2.00e-02 2.50e+03 pdb=" CA ASP G 165 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 125 " -0.033 2.00e-02 2.50e+03 6.37e-02 4.06e+01 pdb=" C SER C 125 " 0.110 2.00e-02 2.50e+03 pdb=" O SER C 125 " -0.040 2.00e-02 2.50e+03 pdb=" N GLU C 126 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 310 " -0.081 2.00e-02 2.50e+03 4.26e-02 3.63e+01 pdb=" CG TYR L 310 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR L 310 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR L 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR L 310 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR L 310 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR L 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 310 " -0.060 2.00e-02 2.50e+03 ... (remaining 3302 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 13 1.94 - 2.68: 1017 2.68 - 3.42: 26643 3.42 - 4.16: 44053 4.16 - 4.90: 79034 Nonbonded interactions: 150760 Sorted by model distance: nonbonded pdb=" CD1 ILE F 354 " pdb=" CA GLU F 398 " model vdw 1.198 3.890 nonbonded pdb=" NH2 ARG A 241 " pdb=" CB LYS F 205 " model vdw 1.534 3.520 nonbonded pdb=" CD1 ILE F 354 " pdb=" CB GLU F 398 " model vdw 1.573 3.860 nonbonded pdb=" O VAL F 263 " pdb=" CA SER F 267 " model vdw 1.574 3.470 nonbonded pdb=" O VAL F 263 " pdb=" N SER F 267 " model vdw 1.612 2.520 ... (remaining 150755 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 126 through 433) selection = (chain 'B' and resid 126 through 433) selection = (chain 'C' and resid 126 through 433) selection = (chain 'D' and resid 126 through 433) selection = (chain 'E' and resid 126 through 433) selection = (chain 'F' and resid 126 through 433) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.600 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 48.260 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 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 : 0.016 0.160 19110 Z= 1.056 Angle : 1.657 25.552 25825 Z= 0.948 Chirality : 0.094 0.551 2984 Planarity : 0.009 0.086 3305 Dihedral : 14.240 172.515 7302 Min Nonbonded Distance : 1.198 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 2.12 % Allowed : 10.88 % Favored : 87.00 % Rotamer: Outliers : 3.62 % Allowed : 6.65 % Favored : 89.74 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.53 (0.14), residues: 2354 helix: -2.82 (0.11), residues: 1296 sheet: -2.56 (0.36), residues: 204 loop : -3.13 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.006 TRP C 206 HIS 0.003 0.001 HIS F 157 PHE 0.036 0.005 PHE C 195 TYR 0.082 0.015 TYR H 310 ARG 0.031 0.003 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 391 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 PHE cc_start: 0.4231 (m-80) cc_final: 0.3994 (m-80) REVERT: B 286 ILE cc_start: 0.8376 (mt) cc_final: 0.8107 (mt) REVERT: D 113 LYS cc_start: 0.7187 (mttt) cc_final: 0.6563 (ptmm) REVERT: D 245 GLU cc_start: 0.6828 (pt0) cc_final: 0.6096 (pm20) REVERT: D 398 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: E 254 THR cc_start: 0.8202 (m) cc_final: 0.7862 (m) REVERT: E 280 TRP cc_start: 0.6494 (p90) cc_final: 0.6069 (p90) REVERT: F 163 ARG cc_start: 0.2433 (ttm170) cc_final: 0.1494 (mmt180) REVERT: F 291 GLU cc_start: 0.3280 (OUTLIER) cc_final: 0.2985 (tt0) REVERT: L 319 GLU cc_start: 0.0087 (OUTLIER) cc_final: -0.0950 (mt-10) outliers start: 74 outliers final: 17 residues processed: 463 average time/residue: 0.3665 time to fit residues: 242.8283 Evaluate side-chains 204 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 370 THR Chi-restraints excluded: chain F residue 397 LYS Chi-restraints excluded: chain F residue 417 VAL Chi-restraints excluded: chain L residue 319 GLU Chi-restraints excluded: chain M residue 314 PRO Chi-restraints excluded: chain N residue 314 PRO Chi-restraints excluded: chain O residue 314 PRO Chi-restraints excluded: chain Q residue 314 PRO Chi-restraints excluded: chain S residue 314 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 359 HIS ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN C 162 ASN C 191 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN C 359 HIS C 427 GLN D 216 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 GLN D 359 HIS ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 216 GLN F 265 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 ASN J 296 GLN ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 GLN ** L 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 GLN ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 296 GLN ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 GLN R 328 ASN ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19110 Z= 0.241 Angle : 0.753 9.284 25825 Z= 0.379 Chirality : 0.045 0.366 2984 Planarity : 0.006 0.066 3305 Dihedral : 10.309 158.612 2664 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.50 % Favored : 93.03 % Rotamer: Outliers : 2.25 % Allowed : 11.88 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.17), residues: 2354 helix: -0.65 (0.14), residues: 1340 sheet: -2.08 (0.36), residues: 215 loop : -2.43 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 206 HIS 0.012 0.002 HIS F 359 PHE 0.022 0.002 PHE D 218 TYR 0.023 0.002 TYR B 295 ARG 0.006 0.001 ARG E 430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 240 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 LEU cc_start: 0.8305 (mt) cc_final: 0.7881 (mp) REVERT: C 158 LEU cc_start: 0.8598 (mt) cc_final: 0.8344 (mt) REVERT: C 245 GLU cc_start: 0.7285 (pt0) cc_final: 0.6868 (mm-30) REVERT: C 411 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7566 (mmmt) REVERT: D 113 LYS cc_start: 0.7417 (mttt) cc_final: 0.6741 (ptmm) REVERT: D 207 MET cc_start: 0.8571 (tpt) cc_final: 0.7942 (tpt) REVERT: D 245 GLU cc_start: 0.7306 (pt0) cc_final: 0.6773 (pm20) REVERT: D 397 LYS cc_start: 0.5670 (OUTLIER) cc_final: 0.5157 (mmtt) REVERT: E 277 ASN cc_start: 0.7032 (m-40) cc_final: 0.6561 (p0) REVERT: E 355 GLN cc_start: 0.5699 (OUTLIER) cc_final: 0.4856 (pm20) REVERT: F 405 ASP cc_start: 0.0928 (OUTLIER) cc_final: 0.0496 (m-30) outliers start: 46 outliers final: 20 residues processed: 272 average time/residue: 0.3204 time to fit residues: 132.2657 Evaluate side-chains 198 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 405 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 214 optimal weight: 9.9990 chunk 231 optimal weight: 50.0000 chunk 191 optimal weight: 5.9990 chunk 212 optimal weight: 50.0000 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN B 277 ASN B 434 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 HIS F 311 ASN ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19110 Z= 0.297 Angle : 0.725 7.957 25825 Z= 0.363 Chirality : 0.045 0.274 2984 Planarity : 0.006 0.062 3305 Dihedral : 9.494 175.035 2628 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.88 % Favored : 92.61 % Rotamer: Outliers : 2.64 % Allowed : 15.00 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2354 helix: 0.24 (0.15), residues: 1300 sheet: -1.78 (0.36), residues: 212 loop : -2.17 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 132 HIS 0.005 0.001 HIS A 359 PHE 0.025 0.003 PHE D 218 TYR 0.028 0.002 TYR B 295 ARG 0.009 0.001 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 247 GLU cc_start: 0.6947 (tm-30) cc_final: 0.5928 (tt0) REVERT: B 252 ILE cc_start: 0.8355 (tt) cc_final: 0.8128 (tt) REVERT: B 390 ASP cc_start: 0.6424 (OUTLIER) cc_final: 0.6160 (t0) REVERT: D 113 LYS cc_start: 0.7358 (mttt) cc_final: 0.6622 (ptmm) REVERT: D 245 GLU cc_start: 0.7565 (pt0) cc_final: 0.7070 (pm20) REVERT: E 277 ASN cc_start: 0.7451 (m-40) cc_final: 0.6613 (p0) REVERT: G 166 GLU cc_start: 0.5191 (tm-30) cc_final: 0.4987 (tm-30) REVERT: F 405 ASP cc_start: 0.2189 (OUTLIER) cc_final: 0.1570 (m-30) outliers start: 54 outliers final: 32 residues processed: 232 average time/residue: 0.3007 time to fit residues: 106.9563 Evaluate side-chains 197 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 8.9990 chunk 161 optimal weight: 0.0030 chunk 111 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 50.0000 chunk 228 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN C 162 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19110 Z= 0.164 Angle : 0.607 8.366 25825 Z= 0.299 Chirality : 0.040 0.194 2984 Planarity : 0.005 0.056 3305 Dihedral : 8.565 167.568 2622 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.35 % Favored : 94.18 % Rotamer: Outliers : 2.30 % Allowed : 16.72 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2354 helix: 0.78 (0.15), residues: 1313 sheet: -1.61 (0.38), residues: 206 loop : -1.81 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 280 HIS 0.005 0.001 HIS A 359 PHE 0.016 0.001 PHE A 360 TYR 0.014 0.001 TYR B 295 ARG 0.006 0.001 ARG F 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 198 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ARG cc_start: 0.6792 (mpt180) cc_final: 0.6378 (mpt180) REVERT: A 400 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6593 (p0) REVERT: B 247 GLU cc_start: 0.6832 (tm-30) cc_final: 0.5861 (tt0) REVERT: B 292 ARG cc_start: 0.7479 (mmt180) cc_final: 0.7258 (mmt-90) REVERT: B 332 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: B 390 ASP cc_start: 0.6342 (OUTLIER) cc_final: 0.5839 (m-30) REVERT: D 113 LYS cc_start: 0.7351 (mttt) cc_final: 0.6628 (ptmm) REVERT: D 207 MET cc_start: 0.8451 (tpt) cc_final: 0.7950 (tpt) REVERT: D 245 GLU cc_start: 0.7475 (pt0) cc_final: 0.7229 (pm20) REVERT: D 296 ILE cc_start: 0.8315 (mm) cc_final: 0.8010 (mm) REVERT: D 325 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6976 (mtm180) REVERT: E 277 ASN cc_start: 0.7045 (m-40) cc_final: 0.6662 (p0) REVERT: E 355 GLN cc_start: 0.6248 (OUTLIER) cc_final: 0.5561 (pm20) outliers start: 47 outliers final: 22 residues processed: 233 average time/residue: 0.2982 time to fit residues: 106.6893 Evaluate side-chains 193 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 355 GLN Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 0.0970 chunk 94 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19110 Z= 0.188 Angle : 0.610 8.328 25825 Z= 0.301 Chirality : 0.040 0.168 2984 Planarity : 0.005 0.051 3305 Dihedral : 7.844 143.985 2619 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.95 % Favored : 93.63 % Rotamer: Outliers : 2.79 % Allowed : 17.79 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2354 helix: 1.12 (0.15), residues: 1311 sheet: -1.44 (0.37), residues: 216 loop : -1.67 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 280 HIS 0.004 0.001 HIS A 359 PHE 0.016 0.002 PHE B 218 TYR 0.018 0.001 TYR B 295 ARG 0.010 0.001 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 189 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ARG cc_start: 0.6776 (mpt180) cc_final: 0.5583 (mpt180) REVERT: A 400 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6806 (p0) REVERT: B 292 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7235 (mmt-90) REVERT: B 332 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: B 390 ASP cc_start: 0.6412 (OUTLIER) cc_final: 0.6060 (m-30) REVERT: D 113 LYS cc_start: 0.7227 (mttt) cc_final: 0.6458 (ptmm) REVERT: D 207 MET cc_start: 0.8363 (tpt) cc_final: 0.7722 (tpt) REVERT: D 245 GLU cc_start: 0.7502 (pt0) cc_final: 0.7255 (pm20) REVERT: D 296 ILE cc_start: 0.8274 (mm) cc_final: 0.7972 (mm) REVERT: E 277 ASN cc_start: 0.7109 (m-40) cc_final: 0.6647 (p0) outliers start: 57 outliers final: 38 residues processed: 230 average time/residue: 0.2942 time to fit residues: 104.0362 Evaluate side-chains 215 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 173 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.7980 chunk 205 optimal weight: 50.0000 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 228 optimal weight: 40.0000 chunk 189 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19110 Z= 0.203 Angle : 0.616 8.384 25825 Z= 0.303 Chirality : 0.041 0.159 2984 Planarity : 0.005 0.052 3305 Dihedral : 7.421 122.242 2619 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.69 % Favored : 93.88 % Rotamer: Outliers : 2.79 % Allowed : 18.08 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.18), residues: 2354 helix: 1.38 (0.15), residues: 1310 sheet: -1.32 (0.38), residues: 218 loop : -1.55 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 280 HIS 0.003 0.001 HIS C 157 PHE 0.016 0.002 PHE B 218 TYR 0.019 0.001 TYR B 295 ARG 0.008 0.001 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 190 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6903 (p0) REVERT: B 292 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7237 (mmt-90) REVERT: B 332 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7924 (tp30) REVERT: B 390 ASP cc_start: 0.6434 (OUTLIER) cc_final: 0.6182 (m-30) REVERT: B 397 LYS cc_start: 0.7179 (tptt) cc_final: 0.6949 (mtpt) REVERT: D 113 LYS cc_start: 0.7175 (mttt) cc_final: 0.6461 (ptmm) REVERT: D 207 MET cc_start: 0.8280 (tpt) cc_final: 0.7690 (tpt) REVERT: D 245 GLU cc_start: 0.7583 (pt0) cc_final: 0.7322 (pm20) REVERT: D 296 ILE cc_start: 0.8315 (mm) cc_final: 0.8002 (mm) REVERT: D 398 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6022 (pt0) REVERT: E 277 ASN cc_start: 0.7104 (m-40) cc_final: 0.6505 (p0) REVERT: E 388 TRP cc_start: 0.3635 (p-90) cc_final: 0.3312 (p-90) REVERT: F 359 HIS cc_start: 0.3746 (OUTLIER) cc_final: 0.2659 (m-70) REVERT: F 411 LYS cc_start: 0.4759 (pttt) cc_final: 0.3716 (tttp) outliers start: 57 outliers final: 40 residues processed: 232 average time/residue: 0.2873 time to fit residues: 104.1059 Evaluate side-chains 218 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 130 optimal weight: 0.0020 chunk 166 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 227 optimal weight: 50.0000 chunk 142 optimal weight: 0.0970 chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN C 216 GLN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19110 Z= 0.151 Angle : 0.577 8.302 25825 Z= 0.282 Chirality : 0.039 0.148 2984 Planarity : 0.004 0.052 3305 Dihedral : 6.939 115.244 2619 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.23 % Favored : 94.39 % Rotamer: Outliers : 2.35 % Allowed : 18.33 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2354 helix: 1.63 (0.15), residues: 1312 sheet: -1.26 (0.37), residues: 224 loop : -1.40 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 280 HIS 0.009 0.001 HIS E 359 PHE 0.014 0.001 PHE A 155 TYR 0.011 0.001 TYR B 295 ARG 0.006 0.000 ARG F 352 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 192 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 LEU cc_start: 0.7983 (mt) cc_final: 0.7722 (mp) REVERT: B 332 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7807 (tp30) REVERT: B 397 LYS cc_start: 0.7516 (tptt) cc_final: 0.6998 (mttt) REVERT: D 113 LYS cc_start: 0.7122 (mttt) cc_final: 0.6447 (ptmm) REVERT: D 172 TYR cc_start: 0.8295 (p90) cc_final: 0.8085 (p90) REVERT: D 207 MET cc_start: 0.8348 (tpt) cc_final: 0.7637 (tpt) REVERT: D 296 ILE cc_start: 0.8280 (mm) cc_final: 0.7960 (mm) REVERT: D 325 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6489 (mtt180) REVERT: D 398 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6038 (pt0) REVERT: F 359 HIS cc_start: 0.3412 (OUTLIER) cc_final: 0.2183 (m-70) REVERT: F 411 LYS cc_start: 0.4704 (pttt) cc_final: 0.3672 (tttp) outliers start: 48 outliers final: 28 residues processed: 222 average time/residue: 0.2928 time to fit residues: 100.2196 Evaluate side-chains 211 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 ASP Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 0.0050 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 178 optimal weight: 0.0270 chunk 206 optimal weight: 20.0000 overall best weight: 1.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN C 162 ASN C 265 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN F 216 GLN ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.5809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19110 Z= 0.210 Angle : 0.617 8.335 25825 Z= 0.303 Chirality : 0.041 0.148 2984 Planarity : 0.005 0.054 3305 Dihedral : 7.011 110.410 2617 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.50 % Favored : 93.25 % Rotamer: Outliers : 2.30 % Allowed : 18.62 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2354 helix: 1.64 (0.15), residues: 1321 sheet: -1.19 (0.38), residues: 218 loop : -1.35 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 280 HIS 0.010 0.001 HIS E 359 PHE 0.014 0.002 PHE B 218 TYR 0.019 0.001 TYR B 295 ARG 0.005 0.000 ARG F 352 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 LEU cc_start: 0.8123 (mt) cc_final: 0.7808 (mp) REVERT: B 332 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: B 397 LYS cc_start: 0.7668 (tptt) cc_final: 0.7247 (mttt) REVERT: D 113 LYS cc_start: 0.7106 (mttt) cc_final: 0.6297 (ptmm) REVERT: D 207 MET cc_start: 0.8258 (tpt) cc_final: 0.7685 (tpt) REVERT: D 296 ILE cc_start: 0.8305 (mm) cc_final: 0.8019 (mm) REVERT: D 325 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6771 (mtt90) REVERT: D 398 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6081 (pt0) REVERT: D 430 ARG cc_start: 0.7127 (ttp80) cc_final: 0.6680 (ttp80) REVERT: F 359 HIS cc_start: 0.3432 (OUTLIER) cc_final: 0.2250 (m-70) REVERT: F 411 LYS cc_start: 0.4882 (pttt) cc_final: 0.3932 (tttp) outliers start: 47 outliers final: 30 residues processed: 207 average time/residue: 0.3010 time to fit residues: 96.7600 Evaluate side-chains 206 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 50.0000 chunk 198 optimal weight: 9.9990 chunk 211 optimal weight: 30.0000 chunk 127 optimal weight: 0.0370 chunk 92 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 191 optimal weight: 30.0000 chunk 200 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN C 265 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.5948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19110 Z= 0.184 Angle : 0.598 8.300 25825 Z= 0.292 Chirality : 0.040 0.159 2984 Planarity : 0.005 0.054 3305 Dihedral : 6.867 105.740 2617 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.56 % Favored : 94.22 % Rotamer: Outliers : 1.96 % Allowed : 18.96 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 2354 helix: 1.73 (0.15), residues: 1323 sheet: -1.15 (0.38), residues: 218 loop : -1.28 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 280 HIS 0.010 0.001 HIS E 359 PHE 0.016 0.001 PHE F 308 TYR 0.015 0.001 TYR B 295 ARG 0.005 0.000 ARG F 352 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 LEU cc_start: 0.7994 (mt) cc_final: 0.7733 (mp) REVERT: B 332 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: B 397 LYS cc_start: 0.7753 (tptt) cc_final: 0.7260 (mttt) REVERT: B 402 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7202 (p) REVERT: D 113 LYS cc_start: 0.7120 (mttt) cc_final: 0.6292 (ptmm) REVERT: D 207 MET cc_start: 0.8262 (tpt) cc_final: 0.7629 (tpt) REVERT: D 296 ILE cc_start: 0.8276 (mm) cc_final: 0.7962 (mm) REVERT: D 325 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6714 (mtt90) REVERT: D 398 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6107 (pt0) REVERT: F 292 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6278 (mmp80) REVERT: F 359 HIS cc_start: 0.3286 (OUTLIER) cc_final: 0.2133 (m-70) REVERT: F 411 LYS cc_start: 0.4890 (pttt) cc_final: 0.3938 (tttp) outliers start: 40 outliers final: 29 residues processed: 209 average time/residue: 0.3162 time to fit residues: 100.4498 Evaluate side-chains 209 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 155 optimal weight: 0.4980 chunk 235 optimal weight: 50.0000 chunk 216 optimal weight: 30.0000 chunk 187 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19110 Z= 0.199 Angle : 0.610 8.378 25825 Z= 0.300 Chirality : 0.041 0.154 2984 Planarity : 0.005 0.055 3305 Dihedral : 6.961 131.391 2617 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.24 % Favored : 93.54 % Rotamer: Outliers : 1.91 % Allowed : 19.16 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2354 helix: 1.84 (0.15), residues: 1301 sheet: -1.14 (0.38), residues: 217 loop : -1.25 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 280 HIS 0.010 0.001 HIS E 359 PHE 0.039 0.002 PHE F 308 TYR 0.018 0.001 TYR B 295 ARG 0.007 0.000 ARG F 352 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4708 Ramachandran restraints generated. 2354 Oldfield, 0 Emsley, 2354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 SER cc_start: 0.6872 (m) cc_final: 0.6628 (p) REVERT: B 257 LEU cc_start: 0.8028 (mt) cc_final: 0.7757 (mp) REVERT: B 332 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: B 402 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7112 (p) REVERT: D 113 LYS cc_start: 0.7111 (mttt) cc_final: 0.6290 (ptmm) REVERT: D 207 MET cc_start: 0.8236 (tpt) cc_final: 0.7635 (tpt) REVERT: D 296 ILE cc_start: 0.8294 (mm) cc_final: 0.7962 (mm) REVERT: D 398 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.5905 (pt0) REVERT: D 430 ARG cc_start: 0.6696 (ttp80) cc_final: 0.6356 (ttp80) REVERT: F 292 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6318 (mmp80) REVERT: F 304 ARG cc_start: 0.6295 (mtm-85) cc_final: 0.6026 (ttp-110) REVERT: F 318 VAL cc_start: 0.3922 (p) cc_final: 0.3646 (t) REVERT: F 359 HIS cc_start: 0.3153 (OUTLIER) cc_final: 0.2036 (m-70) REVERT: F 411 LYS cc_start: 0.5043 (pttt) cc_final: 0.4006 (tttp) outliers start: 39 outliers final: 30 residues processed: 212 average time/residue: 0.3144 time to fit residues: 103.0719 Evaluate side-chains 213 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 418 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 292 ARG Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 359 HIS Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 390 ASP Chi-restraints excluded: chain I residue 294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.0470 chunk 172 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 78 optimal weight: 0.0000 chunk 192 optimal weight: 10.0000 chunk 23 optimal weight: 0.0370 chunk 34 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN ** H 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.235896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.202803 restraints weight = 30208.633| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.43 r_work: 0.4064 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.4050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19110 Z= 0.169 Angle : 0.587 7.901 25825 Z= 0.288 Chirality : 0.040 0.154 2984 Planarity : 0.005 0.055 3305 Dihedral : 6.783 126.746 2617 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.10 % Favored : 94.69 % Rotamer: Outliers : 1.71 % Allowed : 19.35 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.19), residues: 2354 helix: 1.94 (0.15), residues: 1305 sheet: -1.13 (0.37), residues: 224 loop : -1.18 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 388 HIS 0.010 0.001 HIS E 359 PHE 0.062 0.002 PHE F 308 TYR 0.014 0.001 TYR B 295 ARG 0.007 0.000 ARG F 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3592.92 seconds wall clock time: 66 minutes 10.17 seconds (3970.17 seconds total)