Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 15 17:47:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/08_2023/6ap1_8887_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/08_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_8887/08_2023/6ap1_8887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/08_2023/6ap1_8887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/08_2023/6ap1_8887_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ap1_8887/08_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 9.76, per 1000 atoms: 0.52 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: 7.82 Conformation dependent library (CDL) restraints added in 2.9 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: 2.80 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: 5.14 Time building geometry restraints manager: 8.35 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.200 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 48.640 Find NCS groups from input model: 1.540 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.630 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.280 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: 0.3782 time to fit residues: 250.3376 Evaluate side-chains 199 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 5 residues processed: 17 average time/residue: 0.2203 time to fit residues: 9.2016 ------------------------------------------------------------------------------- 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 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 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: 0.5752 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 19110 Z= 0.243 Angle : 0.758 9.486 25825 Z= 0.381 Chirality : 0.045 0.371 2984 Planarity : 0.006 0.066 3305 Dihedral : 9.713 159.835 2614 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.41 % Favored : 93.12 % Rotamer Outliers : 1.96 % 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: -2.03 (0.36), residues: 214 loop : -2.44 (0.21), residues: 800 *********************** 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 284 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 244 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 272 average time/residue: 0.3149 time to fit residues: 130.2965 Evaluate side-chains 187 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 2.225 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1719 time to fit residues: 8.3161 ------------------------------------------------------------------------------- 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: 0.5980 chunk 178 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 231 optimal weight: 50.0000 chunk 191 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 172 optimal weight: 0.0980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 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 ** 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** ** 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: 0.5809 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19110 Z= 0.214 Angle : 0.660 8.802 25825 Z= 0.328 Chirality : 0.042 0.242 2984 Planarity : 0.005 0.062 3305 Dihedral : 8.882 179.105 2614 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.24 % Favored : 93.25 % Rotamer Outliers : 1.76 % 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: -1.06 (0.18), residues: 2354 helix: 0.40 (0.15), residues: 1300 sheet: -1.84 (0.34), residues: 243 loop : -2.08 (0.21), residues: 811 *********************** 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 233 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 220 average time/residue: 0.3267 time to fit residues: 108.3080 Evaluate side-chains 174 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1651 time to fit residues: 7.9311 ------------------------------------------------------------------------------- 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: 20.0000 chunk 161 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 50.0000 chunk 228 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** 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: 0.5808 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 19110 Z= 0.173 Angle : 0.607 8.401 25825 Z= 0.300 Chirality : 0.041 0.181 2984 Planarity : 0.005 0.055 3305 Dihedral : 8.473 177.425 2614 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.65 % Favored : 93.88 % Rotamer Outliers : 1.08 % 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: -0.42 (0.18), residues: 2354 helix: 0.86 (0.15), residues: 1329 sheet: -1.69 (0.37), residues: 206 loop : -1.75 (0.21), residues: 819 *********************** 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 209 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 204 average time/residue: 0.3237 time to fit residues: 100.8501 Evaluate side-chains 175 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 2.297 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1735 time to fit residues: 5.4555 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 ** 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.5296 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= 0.348 Angle : 0.740 8.644 25825 Z= 0.369 Chirality : 0.045 0.213 2984 Planarity : 0.006 0.061 3305 Dihedral : 8.872 162.847 2614 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.31 % Favored : 92.27 % Rotamer Outliers : 1.66 % 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: -0.50 (0.18), residues: 2354 helix: 0.82 (0.15), residues: 1305 sheet: -1.58 (0.38), residues: 205 loop : -1.81 (0.21), residues: 844 *********************** 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 212 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 2.416 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 204 average time/residue: 0.3140 time to fit residues: 97.8358 Evaluate side-chains 181 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 2.049 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1684 time to fit residues: 8.6783 ------------------------------------------------------------------------------- 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: 1.9990 chunk 205 optimal weight: 50.0000 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 189 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.0670 chunk 119 optimal weight: 9.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 19110 Z= 0.228 Angle : 0.638 8.357 25825 Z= 0.316 Chirality : 0.042 0.195 2984 Planarity : 0.005 0.054 3305 Dihedral : 8.160 149.646 2614 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.73 % Favored : 93.84 % Rotamer Outliers : 0.64 % 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: -0.09 (0.18), residues: 2354 helix: 1.18 (0.15), residues: 1307 sheet: -1.55 (0.38), residues: 206 loop : -1.65 (0.21), residues: 841 *********************** 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 202 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 198 average time/residue: 0.3055 time to fit residues: 94.0505 Evaluate side-chains 177 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 2.087 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1789 time to fit residues: 4.7934 ------------------------------------------------------------------------------- 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: 6.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 129 optimal weight: 0.0570 chunk 192 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 227 optimal weight: 50.0000 chunk 142 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- 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 265 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN E 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** ** 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: 0.5916 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19110 Z= 0.201 Angle : 0.621 8.398 25825 Z= 0.306 Chirality : 0.041 0.165 2984 Planarity : 0.005 0.053 3305 Dihedral : 7.612 129.386 2614 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.50 % Favored : 93.16 % Rotamer Outliers : 0.88 % 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: 0.21 (0.18), residues: 2354 helix: 1.45 (0.15), residues: 1307 sheet: -1.46 (0.38), residues: 206 loop : -1.54 (0.21), residues: 841 *********************** 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 200 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 193 average time/residue: 0.3141 time to fit residues: 93.0677 Evaluate side-chains 174 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1762 time to fit residues: 6.3539 ------------------------------------------------------------------------------- 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: 0.0980 chunk 90 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN D 191 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN F 162 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5887 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19110 Z= 0.168 Angle : 0.595 8.356 25825 Z= 0.291 Chirality : 0.040 0.152 2984 Planarity : 0.005 0.053 3305 Dihedral : 7.195 117.403 2614 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.69 % Favored : 94.01 % Rotamer Outliers : 0.59 % 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: 0.46 (0.18), residues: 2354 helix: 1.61 (0.15), residues: 1323 sheet: -1.41 (0.38), residues: 206 loop : -1.41 (0.22), residues: 825 *********************** 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 199 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 194 average time/residue: 0.3239 time to fit residues: 95.4332 Evaluate side-chains 177 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1768 time to fit residues: 5.4905 ------------------------------------------------------------------------------- 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: 30.0000 chunk 198 optimal weight: 3.9990 chunk 211 optimal weight: 20.0000 chunk 127 optimal weight: 0.0060 chunk 92 optimal weight: 0.9990 chunk 166 optimal weight: 0.0170 chunk 65 optimal weight: 0.5980 chunk 191 optimal weight: 20.0000 chunk 200 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 overall best weight: 0.5034 ------------------------------------------------------------------------------- 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 265 ASN D 191 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.6039 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= 0.149 Angle : 0.577 8.358 25825 Z= 0.282 Chirality : 0.040 0.154 2984 Planarity : 0.004 0.054 3305 Dihedral : 6.763 108.799 2614 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.18 % Rotamer Outliers : 0.29 % 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: 0.67 (0.18), residues: 2354 helix: 1.75 (0.15), residues: 1327 sheet: -1.35 (0.38), residues: 212 loop : -1.26 (0.22), residues: 815 *********************** 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 194 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 193 average time/residue: 0.3313 time to fit residues: 97.1154 Evaluate side-chains 179 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 2.101 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1981 time to fit residues: 4.3696 ------------------------------------------------------------------------------- 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: 0.0870 chunk 155 optimal weight: 0.6980 chunk 235 optimal weight: 30.0000 chunk 216 optimal weight: 40.0000 chunk 187 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 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 0.046 19110 Z= 0.170 Angle : 0.592 8.434 25825 Z= 0.290 Chirality : 0.040 0.169 2984 Planarity : 0.004 0.055 3305 Dihedral : 6.702 121.302 2614 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.78 % Favored : 94.01 % Rotamer Outliers : 0.15 % 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: 0.69 (0.18), residues: 2354 helix: 1.76 (0.15), residues: 1326 sheet: -1.37 (0.38), residues: 212 loop : -1.22 (0.22), residues: 816 ********************** 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 174 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 173 average time/residue: 0.3260 time to fit residues: 86.7621 Evaluate side-chains 167 residues out of total 2046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1637 time to fit residues: 3.9953 ------------------------------------------------------------------------------- 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: 0.9990 chunk 172 optimal weight: 20.0000 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 164 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 265 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.236098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.203920 restraints weight = 30538.714| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 4.16 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4333 r_free = 0.4333 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4333 r_free = 0.4333 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.4333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.6228 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= 0.165 Angle : 0.583 8.385 25825 Z= 0.285 Chirality : 0.040 0.153 2984 Planarity : 0.004 0.055 3305 Dihedral : 6.636 127.491 2614 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.18 % Rotamer Outliers : 0.15 % 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: 0.79 (0.18), residues: 2354 helix: 1.83 (0.15), residues: 1326 sheet: -1.33 (0.37), residues: 212 loop : -1.16 (0.22), residues: 816 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.53 seconds wall clock time: 60 minutes 59.96 seconds (3659.96 seconds total)