Starting phenix.real_space_refine on Mon Dec 11 19:17:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/12_2023/6ap1_8887_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/12_2023/6ap1_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_8887/12_2023/6ap1_8887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/12_2023/6ap1_8887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/12_2023/6ap1_8887_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/12_2023/6ap1_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.00, 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: 7.54 Conformation dependent library (CDL) restraints added in 3.8 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: 3.54 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: 5.64 Time building geometry restraints manager: 8.23 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=" C LEU G 172 " pdb=" N NH2 G 173 " ideal model delta sigma weight residual 2.329 1.325 1.004 1.40e-02 5.10e+03 5.14e+03 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 ... (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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.450 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 51.250 Find NCS groups from input model: 1.550 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.430 ------------------------------------------------------------------------------- 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 : 0.018 1.004 19110 Z= 1.135 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 : 2.217 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 outliers start: 74 outliers final: 17 residues processed: 463 average time/residue: 0.3700 time to fit residues: 245.0133 Evaluate side-chains 199 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 5 residues processed: 17 average time/residue: 0.2241 time to fit residues: 9.5995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B 359 HIS 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 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 ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 GLN R 328 ASN S 328 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19110 Z= 0.247 Angle : 0.758 9.461 25825 Z= 0.384 Chirality : 0.045 0.352 2984 Planarity : 0.006 0.068 3305 Dihedral : 9.734 158.697 2614 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.24 % Favored : 93.29 % Rotamer: Outliers : 2.15 % Allowed : 11.93 % Favored : 85.92 % 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: -2.16 (0.17), residues: 2354 helix: -0.66 (0.14), residues: 1340 sheet: -2.03 (0.36), residues: 214 loop : -2.44 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 206 HIS 0.014 0.002 HIS F 359 PHE 0.024 0.002 PHE D 218 TYR 0.022 0.002 TYR B 295 ARG 0.007 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 289 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 17 residues processed: 275 average time/residue: 0.3114 time to fit residues: 130.0799 Evaluate side-chains 191 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1785 time to fit residues: 8.8569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 178 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 231 optimal weight: 50.0000 chunk 191 optimal weight: 50.0000 chunk 212 optimal weight: 40.0000 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 0.1980 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 359 HIS ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19110 Z= 0.192 Angle : 0.643 8.099 25825 Z= 0.319 Chirality : 0.042 0.232 2984 Planarity : 0.005 0.062 3305 Dihedral : 8.839 176.479 2614 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.99 % Favored : 93.50 % Rotamer: Outliers : 1.61 % Allowed : 14.17 % Favored : 84.21 % 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: -1.05 (0.18), residues: 2354 helix: 0.38 (0.15), residues: 1304 sheet: -1.74 (0.36), residues: 217 loop : -2.09 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 280 HIS 0.006 0.001 HIS A 359 PHE 0.017 0.002 PHE B 195 TYR 0.017 0.001 TYR B 295 ARG 0.012 0.001 ARG D 430 *********************** 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 230 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 218 average time/residue: 0.3482 time to fit residues: 113.2661 Evaluate side-chains 179 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1720 time to fit residues: 8.2729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 9.9990 chunk 161 optimal weight: 0.0980 chunk 111 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 228 optimal weight: 50.0000 chunk 112 optimal weight: 0.8980 chunk 204 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 0.4663 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= 0.190 Angle : 0.615 8.319 25825 Z= 0.305 Chirality : 0.041 0.202 2984 Planarity : 0.005 0.055 3305 Dihedral : 8.594 174.566 2614 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.07 % Favored : 93.46 % Rotamer: Outliers : 1.03 % Allowed : 15.98 % Favored : 82.99 % 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: -0.47 (0.18), residues: 2354 helix: 0.83 (0.15), residues: 1318 sheet: -1.53 (0.37), residues: 212 loop : -1.84 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 206 HIS 0.004 0.001 HIS A 359 PHE 0.017 0.002 PHE D 218 TYR 0.018 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 210 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 204 average time/residue: 0.3212 time to fit residues: 100.1478 Evaluate side-chains 174 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1706 time to fit residues: 5.3164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 C 162 ASN C 359 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 427 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** ** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 19110 Z= 0.367 Angle : 0.764 9.260 25825 Z= 0.382 Chirality : 0.046 0.239 2984 Planarity : 0.006 0.064 3305 Dihedral : 9.107 162.978 2614 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.18 % Favored : 92.40 % Rotamer: Outliers : 1.76 % Allowed : 17.79 % Favored : 80.45 % 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: -0.64 (0.18), residues: 2354 helix: 0.69 (0.15), residues: 1308 sheet: -1.59 (0.38), residues: 206 loop : -1.87 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F 132 HIS 0.007 0.002 HIS E 359 PHE 0.026 0.003 PHE B 218 TYR 0.032 0.002 TYR B 295 ARG 0.006 0.001 ARG A 251 *********************** 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 217 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 207 average time/residue: 0.3050 time to fit residues: 97.7508 Evaluate side-chains 179 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1659 time to fit residues: 7.4884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.8980 chunk 205 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 189 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 119 optimal weight: 9.9990 overall best weight: 0.7714 ------------------------------------------------------------------------------- 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** 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** ** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 0.5479 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= 0.174 Angle : 0.609 8.288 25825 Z= 0.300 Chirality : 0.041 0.206 2984 Planarity : 0.005 0.052 3305 Dihedral : 7.944 143.344 2614 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.31 % Favored : 94.35 % Rotamer: Outliers : 0.88 % Allowed : 18.57 % Favored : 80.55 % 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: -0.05 (0.18), residues: 2354 helix: 1.21 (0.15), residues: 1310 sheet: -1.37 (0.38), residues: 212 loop : -1.69 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 132 HIS 0.006 0.001 HIS E 359 PHE 0.014 0.001 PHE B 218 TYR 0.016 0.001 TYR B 295 ARG 0.005 0.000 ARG F 352 *********************** 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 206 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 203 average time/residue: 0.3103 time to fit residues: 97.5510 Evaluate side-chains 179 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1748 time to fit residues: 5.9061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 50.0000 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 GLN C 162 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN E 311 ASN F 162 ASN ** F 355 GLN ** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19110 Z= 0.293 Angle : 0.688 8.328 25825 Z= 0.342 Chirality : 0.043 0.189 2984 Planarity : 0.005 0.056 3305 Dihedral : 8.051 132.697 2614 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.39 % Favored : 92.31 % Rotamer: Outliers : 1.22 % Allowed : 19.35 % 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: -0.02 (0.18), residues: 2354 helix: 1.23 (0.15), residues: 1307 sheet: -1.43 (0.39), residues: 206 loop : -1.62 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 132 HIS 0.004 0.001 HIS A 359 PHE 0.020 0.002 PHE B 159 TYR 0.024 0.002 TYR B 295 ARG 0.005 0.001 ARG A 116 *********************** 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 192 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 183 average time/residue: 0.3344 time to fit residues: 94.0100 Evaluate side-chains 174 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2032 time to fit residues: 7.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 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** ** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19110 Z= 0.210 Angle : 0.628 8.247 25825 Z= 0.310 Chirality : 0.041 0.175 2984 Planarity : 0.005 0.054 3305 Dihedral : 7.585 123.308 2614 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.95 % Favored : 93.84 % Rotamer: Outliers : 0.68 % Allowed : 19.65 % Favored : 79.67 % 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: 0.26 (0.18), residues: 2354 helix: 1.41 (0.15), residues: 1323 sheet: -1.33 (0.39), residues: 205 loop : -1.46 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 132 HIS 0.003 0.001 HIS E 359 PHE 0.015 0.002 PHE B 218 TYR 0.019 0.001 TYR B 295 ARG 0.007 0.001 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 193 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 188 average time/residue: 0.3342 time to fit residues: 96.1388 Evaluate side-chains 170 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 163 time to evaluate : 2.114 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1811 time to fit residues: 5.3298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 40.0000 chunk 198 optimal weight: 10.0000 chunk 211 optimal weight: 50.0000 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 166 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 191 optimal weight: 8.9990 chunk 200 optimal weight: 0.2980 chunk 139 optimal weight: 1.9990 chunk 224 optimal weight: 20.0000 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 ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN ** D 265 ASN ** 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** ** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.6066 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= 0.200 Angle : 0.620 8.507 25825 Z= 0.306 Chirality : 0.041 0.173 2984 Planarity : 0.005 0.056 3305 Dihedral : 7.304 119.408 2614 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.67 % Favored : 93.12 % Rotamer: Outliers : 0.39 % Allowed : 20.19 % 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: 0.41 (0.18), residues: 2354 helix: 1.55 (0.15), residues: 1318 sheet: -1.27 (0.39), residues: 205 loop : -1.42 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 132 HIS 0.004 0.001 HIS E 359 PHE 0.016 0.002 PHE B 218 TYR 0.018 0.001 TYR B 295 ARG 0.007 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 176 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 173 average time/residue: 0.3147 time to fit residues: 83.9235 Evaluate side-chains 161 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1724 time to fit residues: 4.0217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 235 optimal weight: 40.0000 chunk 216 optimal weight: 40.0000 chunk 187 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 199 optimal weight: 50.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 216 GLN C 265 ASN D 191 ASN ** D 265 ASN ** 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** ** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19110 Z= 0.244 Angle : 0.650 8.911 25825 Z= 0.322 Chirality : 0.042 0.172 2984 Planarity : 0.005 0.057 3305 Dihedral : 7.386 122.613 2614 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.67 % Favored : 93.12 % Rotamer: Outliers : 0.34 % Allowed : 20.14 % Favored : 79.52 % 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: 0.37 (0.18), residues: 2354 helix: 1.52 (0.15), residues: 1316 sheet: -1.25 (0.39), residues: 205 loop : -1.44 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 132 HIS 0.004 0.001 HIS B 359 PHE 0.055 0.002 PHE F 308 TYR 0.021 0.001 TYR B 295 ARG 0.007 0.001 ARG F 325 ********************** 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 171 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 167 average time/residue: 0.3255 time to fit residues: 84.0636 Evaluate side-chains 162 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 2.140 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1871 time to fit residues: 4.7795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 23 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 265 ASN D 191 ASN ** D 265 ASN ** 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** ** 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** ** Q 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.231575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.199135 restraints weight = 30372.942| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.23 r_work: 0.4033 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4017 r_free = 0.4017 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.4017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19110 Z= 0.298 Angle : 0.702 8.819 25825 Z= 0.349 Chirality : 0.044 0.193 2984 Planarity : 0.005 0.063 3305 Dihedral : 7.631 124.423 2614 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.35 % Favored : 92.44 % Rotamer: Outliers : 0.39 % Allowed : 20.38 % Favored : 79.23 % 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: 0.12 (0.18), residues: 2354 helix: 1.29 (0.15), residues: 1336 sheet: -1.25 (0.39), residues: 205 loop : -1.60 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP E 388 HIS 0.005 0.001 HIS D 359 PHE 0.045 0.002 PHE F 308 TYR 0.024 0.002 TYR B 295 ARG 0.009 0.001 ARG F 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3544.38 seconds wall clock time: 65 minutes 40.28 seconds (3940.28 seconds total)